Arlene Blackman did not enter a plea during Friday’s hearing. She was released on a $25,000 bond and faces a Feb. 16 court hearing.
Police accuse Blackman of punishing the boys aged 8 and 10 after she found them playing in the bathroom.
She had previously warned students that playing was not allowed in the bathroom.
Blackman is the longtime owner of Blackman's Private School in Maraval, a middle-class residential area in northwest Port-of-Spain.