Seay would not have much time to enjoy his new position. The same month Seay passed the bar exam, fighting began in the American Civil War. Immediately Seay enlisted as a volunteer in the Union army. As a private, Seay assisted in the enlistment of 200 men, which become part of the 32nd Missouri Volunteer Infantry commanded by Colonel John C. Phelps. Seay's work during the Civil War earned him several promotions. Seay was promoted successively to captain, major, and lieutenant colonel. Seay would serve the Union army well, fighting in the Battle of Elkhorn Tavern, Battle of Vicksburg, Battle of Jackson, Battle of Chattanooga, Battle of Lookout Mountain, Battle of Missionary Ridge, Battle of Atlanta, Battle of Savannah, Battle of Bentonville, and the Battle of Columbia. Seay's last service came at Raleigh, North Carolina, while general Joseph E. Johnston surrendered. At the conclusion of the war, Seay left the army at the rank of colonel of his regiment.