Fort Breckinridge was destroyed and the site was abandoned in 1861, following removal of the Union garrison at the start of the American Civil War.

Henry McCarty, better known as "Billy the Kid", reportedly settled in the vicinity of Fort Grant in 1876, working as a ranch hand and tending sheep nearby.

In 1877, McCarty killed a local blacksmith at a saloon and gambling house that is now called the Bonita Store, located a few miles from Fort Grant.

Fort Grant was also the departure point for the pay wagons carrying currency during the Wham Paymaster robbery of 1889.

Edgar Rice Burroughs was stationed at Fort Grant in 1896 as an enlisted man after failing the entrance exam for the United States Military Academy at West Point.

In 1912, Arizona gained statehood, and the fort was occupied by the State Industrial School for Wayward Boys and Girls, which modernized most of the buildings.