It closed at the beginning of the American Civil War, when Governor John W. Ellis ordered the corps of cadets to duty as drill masters in Raleigh.

[1] In the spring of 1861, Governor John W. Ellis ordered cadets from the school to Raleigh to serve as drill masters.

Major Daniel H. Hill, who trained at West Point was superintendent of the school at the start of the American Civil War and was elected colonel of the 1st North Carolina Volunteers.

According to an article in the Charlotte Observer from 1889:As at first organized, the session lasted, without intermission, throughout the year, the months of August and September being spent campaigning in the mountains of North Carolina.

The institute provide board, lodging, fuel, lights, washing, arms, equipment, medical attendance, uniforms and all clothing, except underclothes, for $200 per annum.

A Charlotte Observer article from 1915 stated that the "first Confederate flag raised in the city was hoisted there when Fort Sumter fell by the students of the North Carolina Institute.