President Thomas Jefferson personally appointed him (and 3 other young Missouri men) as a United States Military Academy cadet in July 1804. The U.S. Military Academy at West Point, New York, was the first school of engineering in the United States and graduated its first class in 1802. Gratiot was a member of the Class of 1806, the fourth graduating class, and was commissioned in the Corps of Engineers. He became a captain in 1808 and assisted Alexander Macomb in constructing fortifications in Charleston, South Carolina. He returned to his alma mater in 1810 to be commander of the Army garrison at West Point during 1810–1811.