The woman teacher, whose identity is not disclosed by the police, was booked under the stringent Goa Children's Act.
The boy's mother stated that the teacher physically assaulted and mentally harassed her son during the exam hours on October 7.
Police have registered a cognisable offence against the teacher under section 323 (punishment for voluntarily causing hurt) of the IPC and section 8 of the Goa Children's Act, a police official said.
"The statement of the minor boy was recorded in the presence of an NGO and his medical examination was also conducted. Police have already summoned the teacher and further investigation is on," Police Inspector Jivba Dalvi said.