As the American Civil War began in 1861, although his Quaker upbringing made Palmer abhor violence, his passionate abolitionism compelled him in keeping with the dictates of his conscience to enlist in the Pennsylvania volunteers. Palmer took a commission in the Union Army. He organized the Anderson Troop, an independent company of Pennsylvania cavalry, in the fall of 1861 and was elected its captain. Originally formed to act as a bodyguard for Brig. Gen. Robert Anderson, it instead served as the headquarters cavalry for General Don Carlos Buell, commanding the Army of the Ohio. Impressed with the "elite scouts" that Palmer had assembled, Buell detailed Palmer and 12 of his men to go back to Pennsylvania to recruit more men to form a battalion around the Anderson Troop that would be known as the "1st Anderson Cavalry".