The 39th Regiment moved back to Knoxville shortly after it was mustered in and went into camp at the old fairgrounds. During July and August, 1862, the regiment was detailed by companies to guard bridges, stores, and the line of communication from Bristol to Chattanooga along the East Tennessee & Virginia and the East Tennessee & Georgia railroads. Officially, the regiment was reported to be in General Alexander W Reynolds's brigade of General Carter I. Stevenson's division. Department of East Tennessee. In August, 1862, General 2. Kirby Smith, commander of the department, began moving against the Federal force at Cumberland Gap. Finding the Federals too strong, General Smith left Stevenson's division to contain the enemy at Cumberland Gap while he Smith moved north with the remainder of his command on August 24 to support General Braxton Bragg's invasion of Kentucky. On August 30 Smith routed a force of green Federal troops at Richmond, Kentucky, and on September 1, he entered Lexington. The Federals evacuated Cumberland Gap on September 17, and the 34th Regiment, which was as or near Baptist Gap, Tennessee, took pact in the pursuit of the retreating enemy. On September 19 Stevenson's division marched to join Smith in Kentucky, and on October 2 Smith's reunited force encamped at Frankfort.

General Bragg's defeat by a greatly superior Federal army at Perryville on October 8, brought his and Smith's invasion of Kentucky to an abrupt end. Smith's corps retired to Harrodsburg. Kentucky, on October 1 and established a defensive line, the Federals did not offer battle Reynolds's brigade retreated with Stevenson's division through Cumberland Gap and encamped at Beanys Station. Tennessee, on October 25. By the end of the month the 39th Regiment was reported it Reynolds's brigade of General Henry Hethys division. The regiment encamped in Lenior's Station on the East Tennessee & Georgia Railroad after its return to east Tennessee.

In late December, 1862, a Federal army under General William Rosecrans moved south from Nashville against Bragg's concentrated force at Murfreesboro, There Bragg had taken a position astride the shallow waters of Stone's River with William J. Hardee's corps on the east bank the right of Bragg's line) and Leonidas Polk's corps on the west bank. Before the battle, Reynolds brigade was ordered in Vicksburg, but the 39th Regiment was diverted to Murfreesboro, After waiting in vain for an expected Federal advance on December 30, Bragg decided to attack the Federal right the next day and moved two divisions west of the river, At the same time, Rosecrans was making plans for an assault of his own on skit Confederate right.

Bragg struck first on the morning of December 31 and, after hard fighting, forced the Federal right wing back to a position perpendicular to the Federal center and parallel to the river. Rosecrans then canceled his scheduled attack, called up reinforcements, and by early afternoon had fought the Confederates to a standstill. Two more determined Confederate assaults in she late afternoon were repulsed with heavy casualties to the attackers. During the early stages of the battle the 39th Regiment was engaged near the Nashville & Chattanooga Railroad in General Daniel S. Donelson's brigade, which suffered "frightful losses" in its initial attack After she first assault, the regiment attached itself to General J. Patton Anderson's brigade, which was also engaged in heavy fighting. Both Colonel Coleman and Lieutenant Colonel Hugh H. Davidson were wounded, and command of skis regiment devolved upon Captain Alfred W. Bell of Company B.

Company I was detailed to load ammunition wagons at Murfreesboro during part of the day but later rejoined the regiment on the battlefield. The next day, January 1, 1863, Rosecrans pushed a force across the east bank of Stone's River, and inconclusive fighting continued all along she line. On January 2 Bragg suffered heavy casualties in attacking the Federals on the east bank. The 39th Regiment was assigned to General Arthur M. Manigaultys brigade that evening. Bragg abandoned the field on January 3 and withdrew in the direction of Shelbyville. During the Battle of Murfreesboro, known also as Stone's River, the 39th Regiment lost 2 men killed, 36 wounded, and 6 missing. The regiment was complimented for "good service" by the colonel of the 16th Regiment Tennessee Infantry while fighting in support of that unit, and it was allowed to imprint inverted cannon on its battleflag as a symbol of its part in the capture of enemy artillery during the fighting on December 31.

At Shelbyville, Bragg's army established a defensive position and began reorganizing. On January 21 the 39th Regiment was transferred to Robert B. Vance's brigade, John P. McCown's division, E. Kirby Smith's corps. In addition to the 39th Regiment, the brigade was composed of the 29th Regiment N.C. Troops, the 3rd Battalion Georgia Infantry, and the 9th Regiment Georgia Infantry. Vance's health prevented him from assuming active field command, and General William B. Bate was assigned to command the brigade. At the same time, General Alexander F. Stewart replaced McCown as division commander. Thus the 39th Regiment was in Bateys brigade, Stewart's division, Smith's corps.

The 39th Regiment remained at Shelbyville until May 12, 1863, when it and the 29th Regiment N.C. Troops were ordered to Mississippi. The regiments arrived at Jackson on May 18, two days after the Federals evacuated the town, and were then marched thirty miles to Canton, where General Joseph E. Johnston was organizing an army so relieve the besieged Mississippi River town of Vicksburg

The 39th Regiment was assigned to General Evander McNair's brigade of Samuel U. French's division, Department of Mississippi and East Louisiana. The regiment then moved with McNair's brigade to Birdsong's Farm, near Vicksburg: however, the Vicksburg garrison surrendered to General Ulysses S. Grant on July 4 before Johnston could get his army into position. The 39th Regiment was at the Big Black River when word came of the fall of Vicksburg. Johnston then retired to Jackson, Mississippi. where he occupied previously constructed fieldwork's. French's division held the left-center of the Confederate line, and the 39th Regiment occupied a position just west of the New Orleans, Jackson & Great Northern Railroad. Three corps of Grant's army, under General William T. Sherman, arrived before Johnston's position on July 9 and began siege operations. Active skirmishing and some cannonading continued until July I6, when Johnston withdrew his army over the Pearl River and fell back to Brandon.

White the 39th Regiment was encamped at Brandon. the Federal army in Tennessee under General Rosecrans pushed three widely separated columns into the mountains in pursuit of Bragg, causing the latter to retire from Chattanooga on September 7-8. McNair brigade, along with other Confederate troops in Mississippi, was sent to reinforce Bragg. Upon their arrival, McNair's men were placed in the division of General Bushrod R Johnson, which also contained brigades commanded by General John Gregg and Colonel John S. Fulton.

On the morning of September 19, by which time Rosecrans had succeeded in reuniting most of his divided command behind the west branch of Chickamauga Creek, heavy and extremely confused fighting broke out between the two armies and lasted the rest of the day. At noon the 39th North Carolina and the 25th Regimens Arkansas Infantry were ordered to the support of Gregg's brigade. Moving forward, the two regiments "charged impetuously with loud cheers, passing over the left of Gregg's brigade, and drove the enemy in rapid flight through the thick woods, across the Chattanooga road, pass the small house 100 yards on, and into the corn fields beyond, making a distance altogether of about three-quarters of a mile." (Official Records, Series I. Volume XXX, part 2, pages 499-500,) Finding themselves in as exposed position with a dwindling supply, of ammunition, the exhausted men of the 39th North Carolina and 25th Arkansas fell back to the woods to re-form. After a fresh line of advance moved through the woods, the two regiments marched to their original position and rejoined McNairs brigade. The day ended without either tide having gained a clear advantage. During the night General James Longstreet, whose corps had been dispatched from the Army of Northern Virginia to reinforce Bragg, arrived and was given command of the Confederate left wing.

The next day a Confederate attack on the Federal left was stalemated with heavy casualties, but an attack by Longstreet on the Federal right struck a gap in the enemy line and precipitated a near-rout. Only the stubborn and courageous defense of General George H. Thomas's corps. aided by the timely arrival of two reserve brigades, prevented a Federal disaster. McNair brigade, fighting on the Confederate left under Longstreet, repulsed an enemy attack at about 9:30 am. and, advancing with the rest of the left wing, "drove the enemy steadily and rapidly back, passing over two successive lines of temporary breastworks, a distance of about three-quarters of a mile, reaching the corner of the field, at the opposite end of which were two batteries of the enemy on a hill commanding the whole advance." (Official Records, Series I, Volume XXX, part 2, page 500.)

About that time General McNair was wounded and Colonel Coleman of the 39th Regiment assumed command of the brigade. Coleman reported that the brigade, which was "already in advance of the line, charged furiously upon the batteries diagonally on the right and captured them, taking ten pieces, eight of which were immediately sent with their remaining horses to the rear, and the remaining two, then in the woods, were carried to the rear afterward, the ground never having been reoccupied by the enemy." (Official Records, Source I, Volume XXX, pars 2, page 500.)

As a result of that charge, the brigade found itself in advance of the Confederate line and retired to procure ammunition before going back into line on the left of Jerome B. Robertson's brigade. After Advancing for about half a mile, McNair (Coleman's) men went into position supporting the brigade of Colonel Fulton. The line was then ordered forward. McNair Coleman's) brigade "charged over the hill upon the enemy, and after a protracted and obstinate resistance . . . the enemy were driven from the position." (Official Records, Series I, Volume XXX, part 2, page 501.) Of the 247 members of the 39th Regiment who went into action on September 19, 100 were killed or wounded and three were reported missing during the two-day battle. For its part in the capture of the Federal artillery pieces, the regiment was authorized to imprint additional cannon on its battleflag. Rosecrans's defeated army escaped into the fortifications around Chattanooga.

Following the Battle of Chickamauga, the 39th Regiment, with McNair brigade, rejoined Joseph E. Johnston's army in Mississippi. There it was assigned to French's division at Meridian, where it remained until the division moved to Brandon on December 5. On December 16 General Johnston was ordered to take command of the Army of Tennessee at Dalton, Georgia. and General Leonidas Polk replaced Johnston as commander of the Department of Mississippi and East Louisiana.

French's division remained at Brandon until it was ordered to Jackson to oppose a Federal force consisting of two corps under General Sherman. French occupied the town early on the morning of February 5, 1864, and received word that Sherman was approaching. Realizing that he was heavily outnumbered, French withdrew from Jackson. which was occupied by the Federals that evening. Fearing that Sherman would march next upon Mobile, where a Federal naval attack seemed imminent, Polk ordered elements of French's division to reinforce the garrison there, McNair's brigade and the other troops arrived in Mobile on February 9 and were placed under General Dabney H. Maury, the garrison commander; however, Sherman's objective quickly proved to be Meridian rather than Mobile. and the anticipated naval attack also failed to materialize. Meridian was occupied by the Federals on February 14. The 39th Regiment was then ordered to the Yellow River, Pensacola Bay, Florida. where a Federal attack was expected. Again the expected attack failed to occur, The 39th Regiment went into camp on the Yellow River and busied itself with guard duties, hunting, and fishing. For a brief time, the war was forgotten.

Early in May. 1864, orders came for the 39th Regiment. along with other units of Polk's command, to join Johnston's Army of Tennessee near Dalton. where a powerful Federalarmy under Sherman had started moving south. The 39th Regiment marched to Pollard, Alabama, and from there moved by rail to Resaca, Georgia, just south of Dalton. When is became evident that the main Federal thrust would be against Resaca, Johnston fell back and joined forces there with Polk. The 39th Regimens was placed on the extreme left of the Confederate line and began entrenching on a bluff overlooking the Oustanaula River. Heavy skirmishing, in which the 39th Regimens was involved, broke out at Resaca on May 13, and Sherman launched a major attack the next day. Late on the afternoon of May 14 Polk's corps and the corps of General John B. Hood counterattacked. "We went as a double-quick [one regimental historian related] across a field and just before we entered the timber the command was given to lie down (in order to get our breath), and then forward we went.

In a few moments we were in the thick of the fight, and in less than half an hour it was so dark we could not see, and the enemy's line could be traced by the flash of their guns. The roar of the artillery was deafening, the battle raging along the whole line, and continuing long after nightfall." (Clark's Regiments, Volume II, pages 739-740.) Orders then came down the line for the men to retire to their trenches. and the Confederates broke off the attack.

Dissatisfied with his position, which had been compromised by the loss of several key hills and was in danger of being turned, Johnston withdrew across the Oostanaula on the night of May 15. When the 39th Regiment, the last unit to leave, reached the railroad bridge over which is was to cross the river it found the bridge ablaze in six places but still passable, and the men crossed safely. The regimens rejoined the army at Lay's Ferry and then moved to Calhoun. During the action at Resaca the regiment lost 5 men killed, 8 wounded, and 3 missing.

At Calhoun, Johnston was reinforced by newly arrived units of Polk's army. Johnston then fell back to Adairsville. Kingston, Cassville (where she 39th Regimens was engaged on May 19), Cartersville, and Allatoona Pass. Declining to attack the strong Confederate position at Allatoona Pass, Sherman cut loose from the Western & Atlantic Railroad, the tracks of which he had been following, and marched south toward Dallas in an effort to turn Johnston's left flank.

On May 23 the 39th Regiment was transferred from the brigade formerly commanded by General McNair and Colonel Coleman, and most recently by General Daniel H. Reynolds; the regiment was then assigned to General Matthew D. Ector's brigade of French's division. Also assigned to Ector's command were the 29th Regimens N.C. Troops and four Texas regiments. The 39th Regiment remained in Ector's brigade for the remainder of the war,

In reaction to Sherman's latest maneuver, Johnston withdrew to New Hope Church and Dallas, where he established a new defensive line. Heavy fighting broke out on May 25 and continued intermittently, interspersed with sharp skirmishes, until June 4 when Johnston, to prevent his right flank from being turned, retreated eastward to a prepared position along Lost, Pine, and Brush mountains. During the action at New Hope Church the 39th Regiment loss three men wounded and one missing.

On June 8 Johnston fell back again to a strong position at Kennesaw Mountain, just north of Marietta. One division was left behind at Pine Mountain, several miles in advance of the Kennesaw Mountain line, and it was While observing the enemy from Pine Mountain that General Polk was killed on June 14. Two weeks of mostly small-scale fighting followed, during which both sides were handicapped by inclement weather. In fighting at Lattimer's Mills on June 18, the 39th Regiment lost 6 men killed, 8 wounded, and I missing.

On June 27 Sherman launched a frontal assault against the strongest part of the Confederate line and was repulsed with severe casualties. Some elements of Polk's corps, which was under the temporary command of General William W. Loring, were involved in heavy fighting; however, Ector's brigade was in position on little Kennesaw Mountain, some distance from the primary scene of conflict, and played little part in the battle.

Sherman then reversed to his previous tactic of extending his line beyond the flank of the outnumbered Confederates, and Johnston retired during the night of July 2 to a prepared Position along a ridge behind Knickknack Creek, which crossed the Western & Atlantic Railroad as Smyrna, about 6 miles south of Marietta. Loran's corps was on the right of the line near Smyrna and received the brunt of an attack launched by the Federalize on July 4. Johnston withdrew to a position on the Chattahoochee River. which be occupied on July 5. On July 7 the corps previously commanded by Polk and Loring was assigned to General Alexander P. Stewart. Thus the 39th Regiment was a part of Ector's brigade of French's division of Stewart's corps.

Sherman quickly moved his army up on the track of Johnston, and on July 8 he began fording the Chassahoochee upstream from the Confederate position. Johnston fell back to a defensive position on Peachtree Creek, about four miles north of Atlanta. By July 10 Johnston had established a line that began as the Western & Atlantic Railroad about two miles south of the Chattahoochee River) on the left (west), extended six miles east to the confluence of Peachtree and Pea Vine creeks. and then turned south until it crossed the Georgia Railroad between Atlanta and Decatur.

Stewart's corps was on the left of the line on Peachtree Creek. Johnston's withdrawals through north Georgia during the summer of 1864, although skillful, were both unproductive and self-defeating in the view of Confederate president Jefferson Davis, and on July 17 he replaced Johnston with one of the latter's corps commanders, John B. Hood, Having little option other than to take the offensive, hood launched a furious but poorly conducted, costly, and unsuccessful counterattack on July 20. Ector's brigade was moved from Peachtree Creek into the line on the Marietta road during the early morning hours of July 20, and at noon Ector's and Francis M. Cockrells brigades were sent to the support of General Edward C. WaIthall's division. Ector's men fell back to the entrenchment's just west of the Pace's Ferry road during the night of July 20 and the next day moved farther west beyond the Marietta road.

The 39th Regiments losses on July 20 and during heavy skirmishing on July 19 were fifteen men killed, wounded, and missing. Hood then fell back to the fortifications of Atlanta and prepared to defend the city. Heavy fighting broke out east of Atlanta, in the vicinity of the Georgia Railroad, on July 22. On July 27 Ector's brigade was moved to the left of the Confederate line to a position south of the Turner's Ferry road. The next day it was ordered to reinforce WaIthall's division at Ezra Church, about two miles west of Atlanta. where severe fighting was in progress. There the brigade was placed on the extreme left flank; it returned to the Atlanta trenches at midnight. General Ector was wounded on July 27 and was replaced by Colonel William H. Young of the 9th Regiment Texas Infantry. Colonel Young was appointed brigadier general to rank from August 15.

During August, 1864, Sherman pursued a strategy of extending his lines west of Atlanta in order to cut Hood's railroad communications to the south. Hood sought to match the Federal extensions, and by August 25 the lines had reached the vicinity of the railroad junction at East Point. about four miles southwest of Atlanta, During that time the regiments of Ector's brigade rotated on picket duty in front of the defensive works west of the city.

On August 26 Sherman made a new and powerful thrust to the south that quickly resulted in the severing of both the West Point and the Macon & Western railroads. While Stewart's corps remained behind to hold the Atlanta fortifications, Hood's other two corps, under Hardee and Stephen D. Lee, moved south in an attempt to dislodge the Federals from the Macon & Western Railroad at Jonesboro, about fifteen miles from Atlanta. An unsuccessful two-day battle followed during which two brigades of Hardee's corps were virtually destroyed. Hardee and Lee then retreated to Lovejoy's Station, just south of Jonesboro. There they were joined by Stewart's corps and by Hood, who evacuated Atlanta on September I. French's division served as the rearguard during the retreat. The division went into line at Lovejoy's Station on the afternoon of September 3.

The two armies maintained their positions until September 21 when Hood shifted his forces to Palmetto, about twenty-two miles northwest of Lovejoy's Station. Convinced that Sherman had relinquished the Initiative and intended to rest on his laurels in Atlanta, Hood moved his army northward on October I, to strike the Federal supply line on the Western & Atlantic Railroad. On October 4 General Stewart's corps captured the Federal garrisons as Acworth and Big Shanty, on the railroad just north of Marietta, and tore up fifteen mites of track The next day French's division was sent to capture the major Federal supply depot at Allatoona, about five miles north of Acworth. French's men succeeded in driving the determined Federal defenders from two of their three redoubts but broke off the attack when a false report was received that Federal reinforcements were at hand. French then ordered his men to withdraw. During that action part of the 39th Regiment was sent to protect the artillery while the remainder, a detachment of about forty men, was detailed to support the assault. Two members of the regiment were wounded. General Young was also wounded and captured, and Colonel Coleman again assumed command of the brigade.

Following the Battle of Allatoona, Hood moved his army to the northwest and crossed the Coosa River west of Rome on October 10. Sherman, unable to come to grips with the elusive Hood, moved toward Rossse and ordered General George H. Thomas, who had been sent back to Tennessee with his corps in September, to guard against a Confederate crossing of the Tennessee River west of Chattanooga. Hood then turned back to the northeast, struck the Western & Atlantic Railroad again at Resaca, and advanced on Dalton, where he captured the garrison on October 13. After tearing up twenty miles of track between Resaca and Tunnel Hill, Hood marched west to Gadsden, Alabama. On October 22 he moved to Tuscumbia, Alabama, where he awaited the arrival of supplies before crossing the Tennessee River. Sherman, convinced that Thomas would be able to deal wish Hood, returned with his army to Atlanta and made preparations for his march to the sea.