The accused, identified as Akhilesh Malviya, was thrashed by the parents of the 14-year-old girl, a student of Tilak Middle School, over the alleged incident.
This follows a series of unfortunate events involving children in schools, highlighting the seriousness of school safety in the country.
Police have arrested Malviya under section 354 (assault or criminal force to woman with intent to outrage her modesty) of the IPC and under provisions of Protection of Children from Sexual Offences (POSCO) Act, an official said.
"As the matter is serious, we have arrested Malviya," Kotwali police station Inspector Ajay Nair said.
However, the principal claimed that he was innocent and the charges against him are false.
Further investigation in the case is on, Mr Nair added.
Recently a 7-year-old boy was found murdered in the washroom of Gurgaon's Ryan International School, after he attempted to stop his perpetrator from sexually assaulting him.
A day after this, a 5-year-old was raped allegedly by a peon of the North Delhi school she went to.
The events have led to parents protesting outside various schools, with many schools being brought under scrutiny for not doing required background checks on their employees.