He was preparing to enter Phillips Academy when Carter enlisted as a private in the 22nd Massachusetts Infantry at the start of the American Civil War and remained with the Army of the Potomac from August 5, 1862, until October 4, 1864.

It was during one of these campaigns that he was brevetted first lieutenant and awarded the Medal of Honor for his "most distinguished gallantry" against the Comanche in Blanco Canyon on a tributary of the Brazos River on October 10, 1871.

Carter would suffer a severe injury during the battle, his left leg being shattered as his horse fell against a rock, which would eventually result in his early retirement.

Returning to active duty, he joined Colonel Ranald Mackenzie in several campaigns including against the Kickapoo of northern Mexico in May 1873 and awarded a brevet to captain.

Although he eventually recovered from his leg injury after proper treatment, his requests to return to active service were denied by the US Army; instead he was promoted to captain on the retired list in 1904.