Lori Carmichael Quigley, 41, is charged with three counts of sexual assault upon a person under supervision or discipline, Maj. Danny Lowe said.
All three of the male students at McIntosh Academy were at least 16, Lowe said.
Although 16 is the age of consent in Georgia, the law forbids school personnel from having sex with students.
All of the sexual encounters occurred on school property, Lowe said. He did not elaborate but said Quigley had taught the victims.
Quigley resigned her job a couple of weeks ago but has not admitted any wrongdoing, Lowe said.
She was arrested Friday and has been denied bail, he said.