With the outbreak of the Civil War in early 1861, Ferrero raised a regiment at his own expense, the 51st New York Volunteer Infantry Regiment (the "Shepard Rifles"). He was commissioned as its first colonel and drilled the regiment in military procedures. He led a brigade of three regiments in Maj. Gen. Ambrose Burnside's expedition to Roanoke Island, where his regiment seized the first fortified Confederate redoubt captured in the war. He also commanded a brigade at New Bern under Brig. Gen. Jesse L. Reno.