Upon the outbreak of the American Civil War, Jones readily joined the Union Army. On July 7, 1861, he enlisted with the 37th New York Volunteers, popularly known as the "Irish Rifles", under Colonel John H. McCunn. He was initially a private but quickly found himself elected to the rank of second lieutenant by the men in the regiment. He was present at the First Battle of Bull Run, only two weeks after his enlistment, but saw no action as the unit was held in reserve. Jones displayed "gallant conduct" during his first years with the regiment and soon rose in rank to first lieutenant and adjutant on November 4, 1861, and then major on January 21, 1862. He and the "Irish Rifles" later joined General Samuel P. Heintzelman's III Corps, as part of the 3rd Brigade of the 3rd Division under Brigadier General Philip Kearny, during the Peninsula campaign and participated in Williamsburg, Seven Pines and the Seven Days campaign. Jones was also present when the 37th New York Volunteers, then attached to the 3rd Brigade of the 1st Division of the III Corps, were at the Second Battle of Bull Run. In May and June, he began suffering from malaria and was hospitalized in Washington, D.C. on September 26 remaining there until the end of October. He was also briefly an officer to Major General Franz Sigel prior to the retirement of General Ambrose Burnside and the reorganization of the Army of the Potomac.