In May 1861 Franklin received his commission as a colonel in the 12th U.S. Infantry. Promoted to brigadier general, he led his new brigade into the Battle of First Manassas. He was afterwards promoted to command of a division in the Washington defenses. During the Peninsula campaign he commanded his division, and subsequently, the VI Corps. Later he served in the battles at South Mountain and Antietam. He commanded the Left Grand Division, comprised of two corps, at the Battle of Fredericksburg, and his failure to follow orders led to him being relieved of his command and forced to await new orders. Eventually, he was put in command of XIX Corps in the Red River campaign, in which he was wounded.