The victim's mother, a resident of the village, has alleged that when her son studying in the nursery class of the school did not return home yesterday, she went to the school, police said.
There, she saw a 14-year-old boy of the same village sodomising her son in a bathroom, they said.
The accused managed to escape when the victim's mother reached the bathroom.
A case has been registered and a manhunt launched to nab the accused, police said.