In 1864, before Seelye had reached his 16 birthday, he attempted to enlist as a Union soldier. After repeated rejection by officers who knew his father and his age, he went to Fort Ann and secured acceptance. He ran away from home to Albany and entered the 14th New York Heavy Artillery. His regiment reached the front just after the fall of Petersburg. While on duty in North Carolina, he was thrown from the top of a freight car and received an injury of the spine from which he never fully recovered.