In a suicide note, she accused the teacher of "torturing" her.
Although the girl did not mention period shaming in her letter, the mother says her daughter was asked to leave the class because of the stain.
Menstruation is taboo in parts of rural India. Women are traditionally believed to be impure during their periods.
Police say they have registered a case of suicide and are investigating. The incident took place early on Sunday in Tirunelveli district in the state of Tamil Nadu.