Shafter servedphục asvụ avới 1stcấp lieutenantbậc theTrung úy bậc 1 trong [[QuânTrung độiđoàn LiênBộ bangbinh MiềnTình Bắcnguyện Michigan số 7]] thuộc [[7thQuân Michiganđội VolunteerLiên Infantrybang RegimentMiền Bắc]] attại thecác battlestrận ofđánh [[Trận Ball's Bluff|Ball's Bluff]] và [[Trận Fair Oaks|Fair Oaks]]. Ông bị thương tại [[Trận Fair Oaks]] và sau đó được nhận Huy chương Danh dự vì hành động anh hùng khi chiến đấu. He led a charge on the first day of the battle and was wounded towards the close of that day's fighting. In order to stay with his regiment he concealed his wounds, fighting on the second day of the battle. Ngày 22 tháng 8, 1862 he was mustered out of the volunteer service but returned to the field as major in the [[19th Michigan Volunteer Infantry Regiment]]. He was captured at the [[Trận Thompson's Station]] and spent 3 months in a [[Confederate States Army|Confederate]] prison. In April 1864 after his release he was appointed colonel of the 17th Regiment of [[United States Colored Troops|U.S. Colored Troops]] and led the regiment at the [[Trận Nashville]].
Vào cuối cuộc chiến, ông được thăng làm [[Brevet (military)|brevet]] [[Brigadier general (United States)|brigadier general of volunteers]]. He stayed in the [[Regular Army (United States)|regular army]] when the war ended. During his subsequent service in the [[Indian Wars]], he received his "Pecos Bill" nickname. He led the 24th Infantry, another [[United States Colored Troops]] regiment, in campaigns against the [[Cheyenne]], [[Comanche]], [[Kickapoo people|Kickapoo]] and [[Kiowa]] Indians in [[Texas]]. While commander of [[Fort Davis National Historic Site|Fort Davis]], he started a controversial court-martial of second lieutenant [[Henry Flipper]], the first black cadet to graduate from West Point. In May 1897 he was appointed as a [[Brigadier general (United States)|brigadier general]].
