In 1860, Parnell arrived in the United States and joined the U.S. Army in Brooklyn, New York when the American Civil War began the following year. He became a member of the 4th Regiment New York Volunteer Cavalry, popularly known as "Dickel's Mounted Rifles", serving primarily with the Army of the Potomac. During the first two years of the war, he was part of Colonel Louis Blenker's campaigns in the Shenandoah Valley and West Virginia. He also saw action at the battles of Cross Keys, Port Republic, Cedar Mountain, and the Second Battle of Bull Run. With the Cavalry Corps, he also fought at the battles of Fredericksburg, Beverly Ford, Brandy Station, Stoneman's Raid, Aldie, and Middleburg. On 21 June 1863, he was captured after leading a failed cavalry charge at the Battle of Upperville and briefly held as a prisoner-of-war. He escaped two months later and made his way to Petersburg, West Virginia where he was reunited with his regiment. He later saw action at the battles of the Wilderness, Spotsylvania, Trevilian Station, Petersburg, Lee's Mills, Winchester and Cedar Creek among other engagements.