Left the State October 13, 1861, and during the next eight months was stationed in West Virginia, guarding railroad most of the time. It served next with Shields's Division in the Shenandoah Valley, and was present at the battle of Kernstown, March 23, 1862, but was not actively engaged. It was ordered to the Peninsula in June, arriving there just after the battle of Malvern Hill, and was assigned to Peck's Division, Fourth Corps. Upon the withdrawal from the Peninsula the Thirty-ninth was ordered to Suffolk, where it remained for a few months. The year 1863 was passed at Hilton Head, S.C., and in Charleston Harbor, where it was engaged in the siege operations on Morris Island and at Fort Wagner. Having reënlisted it went home on its veteran furlough, returning in March, 1864, with about 750 men. It was assigned to Howell's (1st) Brigade, Terry's (,st) Division, Tenth Corps, in which it fought during the ensuing campaign against Richmond. In the fighting at Drewry's Bluff and at Bermuda Hundred the regiment lost 14 killed, 110 wounded, and 49 missing; total, 173. The regiment encountered more hard fighting at Deep Bottom, August 16, 1864, where it captured an earth-work, losing in the affair 20 killed, 76 wounded, and 7 missing. In December, 1864, it was transferred to Osborn's (1st) Brigade, Foster's (1st) Division, Twenty-fourth Corps. In the victorious assault on Fort Gregg, at the Fall of Petersburg, the gallantry of the regiment was specially acknowledged by General Gibbon, the corps commander. In that desperate fight it lost 16 killed and 45 wounded, out of only 150 present in action— a part of the regiment having been absent on picket duty; of the nine men in the color-guard, seven were shot down in this assault. The Thirty-ninth was mustered out at Norfolk, Va., in December, 1865.