Appreciative leading Philadelphians presented him a sword upon his return to the city in 1847.  On August 30, 1851, at the age of 49, he was married to Elizabeth McMurtrie.The marriage was a happy one, and at least two sons and one daughter were born to the couple. He retired with 31 years service as colonel and Inspector General of the Army in 1853. He was elected as a member of the American Philosophical Society in 1854. At the beginning of the Civil War, McCall helped organize Pennsylvania volunteers as major general of the state militia and was commissioned brigadier general of volunteers in May 1861. He helped organize and led the famous Pennsylvania Reserves Division, which served as the 2nd Division, I Corps, Army of the Potomac, and 3rd Division, V Corps.
He was one of the oldest West Point graduates to serve in the war. McCall served in the Peninsula Campaign and was wounded and captured at Frayser's Farm, Virginia, in June 1862.While trying to ascertain his position without his staff officers, he instead met the 47th Virginia, part of General James Longstreet's command. Longstreet had served as a brevet Second Lieutenant under Mccall in the 4th U.  He was imprisoned in Libby Prison in Richmond, Virginia. In retirement, McCall farmed in Pennsylvania. He died at his "Belair" estate in West Chester, Pennsylvania on February 25, 1868, and is buried in the Christ Church Burial Ground in his native Philadelphia. McCall School in Society Hill, Center City, Philadelphia is named after him. McCall is commemorated in the scientific name of a species of lizard, Phrynosoma mcallii.