Following the death of Col. Edward D. Baker at Ball's Bluff, Wistar became the commander of the 71st Pennsylvania, and was promoted to colonel on November 11, 1861. The 71st participated in the Peninsular Campaign of 1862, although it isn't clear whether Wistar was actually present; at the Battle of Seven Pines (May 31 and June 1) the regiment was led by its major, and during the Seven Days Battles (June 30 and July 1) commanded by its lieutenant colonel.