The 5-year-old girl had gone to the school washroom where Naushad (20) molested her yesterday, SP (City) Om Prakash Singh said.
He allegedly threatened the child with her life if she disclosed the incident to anyone. Later, she confided in her mother.
Her irate family members and locals indulged in vandalism at the school today.
They were only pacified after police assurance of strict action against the accused, who was later arrested, Singh said.