He was promoted from 1st Sgt. to 2nd Lt. in September 1862, and was severely wounded at the Battle of Second Manassas (Bull Run). Following a long period of recovery he rejoined his unit and was promoted to 1st Lt. on March 1, 1863. Robert Day was promoted to captain of the 56th Pennsylvania Infantry on June 13, 1863, and a few weeks later he was captured on July 1, 1863, on the first day of the Battle of Gettysburg. He was imprisoned with other Union officers in the infamous Libby Prison in Richmond, Virginia.