On the outbreak of the Civil War, Seaver mustered on July 16, 1861, in Newbury, where he was given command of a company in the 3rd Vermont Infantry as a captain, serving until July 1864. He eventually commanded the regiment, and was promoted to major on August 13, 1861; to lieutenant colonel on September 17, 1862; and to full colonel on January 13, 1863. He served in the Battles at Antietam and Gettysburg, among many others. he was mustered out of the service on May 10, 1864.