Since 1852, Morell had served as a colonel in the New York Militia. He was promoted to brigadier general of volunteers on August 9, 1861, and served in brigade and division command in the Army of the Potomac during the Peninsula Campaign. Morell led the 1st Division, V Corps, during most of this period. His close association with Brig. Gen. Fitz John Porter, his corps commander, negatively affected his career prospects, as Porter was court-martialed for dereliction in the Second Battle of Bull Run. Morell testified on Porter's behalf at the court-martial, effectively ruining his military career. After the Battle of Antietam, he saw no additional field service. Morell was appointed a major general on July 4, 1862, but the appointment expired the following year without confirmation by the United States Senate. He commanded the Draft Depot in Indianapolis, Indiana, for most of 1864 and was mustered out from volunteer service on December 15, 1864.