Organized at Davenport, Iowa, in May, 1861. During the first year of its service it was stationed in Missouri, employed on guard duty at various points, and in protecting railroad communications. It left St. Louis February 7, 1862, proceeding by river transports to Fort Donelson, where, under command of Colonel Tuttle, it was engaged in the assault on the enemy's right. It was then in Lauman's Brigade of General C. F. Smith's Division, and led the attack of the brigade. Its casualties at Fort Donelson were 33 killed and 164 wounded; two color-bearers were killed, and two wounded, while eight of the nine men in the color-guard were killed or wounded. The regiment was engaged a few weeks later at Shiloh; it was then in Tuttle's Brigade of W. H. Wallace's Division; loss, 8 killed, 60 wounded, and 4 missing. Next came the Siege of Corinth, and on October 3, 1862, the battle of Corinth. At that battle the Second fought in Hackleman's Brigade of Davies's Division, its loss there amounting to 12 killed, 84 wounded, and 5 missing. Among the killed were Colonel Baker, Lieutenant-Colonel Noah W. Mills and four line officers; General Hackleman was also killed in this engagement.

The regiment wintered at Corinth, Miss, and in the fall of 1863 moved to Pulaski, Tenn. It reenlisted in the winter of 1863-64, and upon its return from its veteran furlough entered the Atlanta campaign, during which it was in Fuller's (1st) Brigade, Veatch's (4th) Division, Sixteenth Corps. After the fall of Atlanta it was transferred to Howard's (1st) Brigade, Rice's (4th) Division, Fifteenth Corps, with which it marched to the Sea and through the Carolinas. In November, 1864, the veterans and recruits of the Third Iowa remaining in the field were transferred to this regiment. The Second Iowa was mustered out July 12, 1865.