In February 1862, Merritt was recalled from service on the frontier to serve as the aide-to-camp to the commander of the cavalry of the Army of the Potomac, General Philip Cooke, and later, General George Stoneman. He served as the commander of the reserves during the raid by Stoneman in the Chancellorsville campaign of May 1863. In June 1863, he was promoted to brigadier general in time to lead a brigade in service at the Battle of Gettysburg. In August 1864 he commanded the Union forces in a skirmish near Front Royal at Guard Hill. In April 1865 during the Appomattox campaign, he served as the second in command to Philip Sheridan and was present at the formal surrender of the Confederate Army of Northern Virginia.
