Thomas Custer was born in New Rumley, Ohio, the third son of Emanuel and Marie Custer. The paternal line was of ethnic German descent. He enlisted in the Union Army, in September 1861, at age 16, and served in the early campaigns of the Civil War as a private in the 21st Ohio Volunteer Infantry. He saw action at numerous battles, including Stones River, Missionary Ridge and the Atlanta Campaign. He mustered out in October 1864 as a corporal. Commissioned a second lieutenant in Company B of the 6th Michigan Cavalry, he became aide-de-camp to his brother George Armstrong Custer and accompanied him throughout the last year of the war.