On July 23, 1861 he was put in command of the 5th Connecticut Volunteer Infantry, and given the rank of colonel. The original regiment was the 1st Regiment Colts Revolving Rifles of Connecticut and was supposed to be led by Samuel Colt, but the unit never took the field. Its organization failing, the regiment was reorganized in May 1861. In early March 1862, Ferry led his troops across the Potomac River, and attacked the Confederates at Winchester, Virginia. This action would later lead to what became the First Battle of Winchester. Ferry was well praised for his ability as a leader and as a military strategist. Ferry was promoted to brigadier general on March 17, 1862. He was then put under the command of General James Shields, whose division joined that of Gen. Irvin McDowell. It was under McDowell that Ferry fought at the First Battle of Winchester. Ferry continued to serve under Shields, during the Valley Campaign.