The teacher, detained for questioning after the complaint was lodged yesterday by the victim's mother, was arrested after he admitted to his guilt during "thorough" questioning, police officials said.
"He has been arrested," Joint Commissioner of Police Hemant Nimbalkar said.
Additional Commissioner of Police (Law and Order) Alok Kumar, "We have thoroughly questioned him."
Police are "fairly sure" about the detained person's involvement, Kumar said, adding "the person is a teacher in the school; he has been with the school for a long time. We have questioned him and he has admitted to his guilt."
The girl, studying in the first standard, was allegedly sexually assaulted twice by the accused on October 28 and 29 within the school premises.
Police had booked a case under Sections 376 of IPC and 5 and 6 of Protection of Children from Sexual Offences Act 2012.
Sec 376 of IPC relates to rape and Sections 4 and 6 of POCSO Act to punishment for penetrative sexual assault and punishment for aggravated penetrative sexual assault, respectively.
Meanwhile, protest broke out in front of the school, where parents and other social organisations demanded answers from its authorities and that police handover the accused to them.
Kumar said the school had not implemented safety measures prescribed by the authorities.