An FIR was registered against the director of Tagore Public School, Bhanwar Lal Choudhary, following which he was arrested in the wee hours, they said.
Protesters torched vehicles, the school office and its rooms late last night demanding immediate arrest of the accused, police said, adding that no case of vandalism has been registered so far.
Police resorted to mild lathi charge to disperse the protesters, they said.
The victim, a senior secondary student, lived in a hostel with 20 other girls. She alleged that Choudhary had molested and attempted to rape her on December 13 when other girls were elsewhere in the hostel, police said.
The accused, who is said to be a government teacher in Macharkhani village, has been running the co-education senior secondary school in Jobner.