Richmond County Board of Education Police Chief Patrick Clayton said surveillance camera footage was key to the swift arrests.
The fire, reported about 4 a.m. Thursday, destroyed the 3,000-square-foot wooden structure.
JROTC uniforms and pellet rifles were damaged in the fire.
The five suspects have been linked to vandalism that occurred at the Hephzibah Community Center earlier Thursday evening and at a concession stand in the football stadium, Clayton said.
James "Trey" Schlein, 19, of the 4800 block of Story Mill Road in Hephzibah, and Antonio Sinkler, 19, of the 2900 block of Old Lake Road in Hephzibah, were arrested on suspicion of first-degree arson and interference with government property.
Burglary charges are expected involving the vandalism at the community center, Clayton said.
Clayton said the three juvenile suspects' names weren't being released because of their age, and they were taken to the Augusta Regional Youth Detention Center.
The investigation involved the board of education, Hephzibah police and the state fire marshal's office.
Officers from the first two agencies were able to identify some of the suspects from their posts at Hephzibah High, Clayton said.