When the war began, Neill served on the staff of the Department of Annapolis and then on the staff of Gen George Cadwalader in the Department of Pennsylvania. Then he was made colonel of the 23rd Pennsylvania Infantry, which he led in Darius Couch’s division of IV Corps Army of the Potomac in the Peninsula Campaign and the Seven Days Battles. Neill was injured in the ankle at the Battle of Malvern Hill. Neill next served under Couch in the Maryland Campaign. He became a brigade commander in the second division of BG Albion Howe in VI Corps at the Battle of Fredericksburg. Neill was promoted to the rank of brigadier general on April 15, 1863, his rank postdated to November 29, 1862. During the Chancellorsville Campaign, Neill brigade led the advance of Howe’s division at the Second Battle of Fredericksburg, also known as the Second Battle of Marye's Heights, when VI Corps, under Maj. Gen. John Sedgwick drove Jubal Early’s division away from the Heights. His brigade also fought in the Battle of Salem Church. Neill had his horse shot from under him in the fight for Scott's Ford, Sedgwick's means of escaping across the Rappahannock River from converging Confederate attacks.