The girl has claimed in her complaint that she was raped multiple times by the accused between 2015 and March 2016, said sub-inspector LB Pawar, Manpada police station.
The accused, identified as Deepak Herole who works in a mall in city, was arrested last night.
The day care centre is run by his sister in their house.
Quoting the complaint, Pawar said Herole molested and raped the girl on several occasions.
Herole has been booked under section 354 (assault or criminal force to woman with intent to outrage her modesty) of IPC and under various sections of Protection of Children from Sexual Offences Act (POCSO).