The alleged incident of Garaponta village took place at an under-construction building adjacent to the school in which the girl studies in class 3.
The accused youth, a neighbour of the girl, lured her with food during the lunch break and took her to the building from where she was found without clothes sometime later, her family members alleged.
The matter came to light when her classmates informed her parents, who live nearby, that she had left the school with the youth and went to the building.
Though the incident occurred on Wednesday, a police complaint was lodged on Friday night and then a medical examination was done, the police said.
Angry locals on Saturday ransacked the house of the accused youth though none of his family members were present there. They put up a road blockade for some time in protest against the incident, the police said.
The girl's father said her classmates informed him that the youth had taken her to the building previously also.