At the outbreak of the Civil War, Capehart left his medical practice in Bridgeport and volunteered for the Union Army. He was appointed regimental surgeon of the 1st West Virginia Cavalry on September 18, 1861. In the latter half of 1863, he participated in the battles of Gettysburg, Bristoe Station, and Mine Run. Upon the recommendations of General Judson Kilpatrick and others, Capehart was made colonel and succeeded Nathaniel P. Richmond, who resigned due to health issues, as commander of the regiment on February 22, 1864.