The school opened in 1859 as the Bunker Hill Academy (and was at the time non-military) but closed during the American Civil War.

In 1883, the military academy was established in the ageing building by Congregational clergyman Reverend Samuel L. Stiver, offering strict instruction to local children as well as the cadets.

Former students, parents, church ministers, editors, businessmen, and former officials of BHMA are among those from whom the Academy received such high acclaim.

In addition, one suit for common wear, rubber shoes, umbrella, bed linens, blankets, toilet articles and underclothes were expected.

BHMA sports teams are mentioned in Carolyn Scroggins' book as having frequently beaten Bunker Hill High School in games.

From "Bunker Hill Military Academy" by Carolyn Scroggins, concerning BHMA's ultimate fate: "Superintendent Stiver died in November, 1910.