Civil War service
At the beginning of the American Civil War in 1861, Wistar chose to follow his home state and the Union cause. He raised a company of men and was elected its captain. Wistar's company was then added to the 71st Pennsylvania Infantry, originally known as the California Regiment. This regiment was organized at Fort Schuyler located in New York. On June 28 Wistar was promoted to the rank of lieutenant colonel, and on July 1 the 71st left for Fortress Monroe on the Virginia Peninsula. On July 22 Wistar and the 71st was then ordered to Washington, D.C., forming part of the capital's defenses until that fall. Wistar participated in the much-publicized Union defeat in the Battle of Ball's Bluff on October 21. In the fight he temporarily led the regiment and was seriously wounded, hit in his right elbow, his jaw, and thigh.
Following the death of Col. Edward D. Baker at Ball's Bluff, Wistar became the commander of the 71st Pennsylvania, 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.
Wistar fought in the Battle of Antietam on September 17, 1862, and was wounded in his left arm. His commander, Oliver O. Howard, reported on Wistar's new injuries, saying "...with his right arm nearly useless from a former wound, had his left disabled." referring to the previous Ball's Bluff wounds. On November 29 Wistar was promoted to brigadier general, and he was assigned to brigade command in the VII Corps beginning on May 16, 1863.
Beginning on July 18, 1863, Wistar commanded the District of Yorktown in Virginia, and that August the post was re-designated as a subdistrict of the Department of Virginia and North Carolina. In April 1864 he briefly was given divisional command of the XVIII in the Army of the James. On May 7 Wistar resumed leading a brigade and participated in the Bermuda Hundred Campaign, but eleven days later he was relieved of duty and replaced by Col. Griffen Stedman.Military historian Ezra J. Warner surmises Wistar performed poorly during this campaign, saying:
The conclusion is more or less inescapable, although nothing concrete appears in the records, that Wistar's handling of his brigade on the foggy morning of May 16 left something to be desired.
Wistar's resignation from the Union Army was accepted by the U.S. War Department on September 15, 1864.