The accused was arrested on Friday after the victim's parents informed the police Thursday.
The incident occurred in the playschool located in west Delhi's Hari Nagar area. The girl was taken to the hospital after she complained of pain in abdomen, police said.
This is the second such incident of rape in the past two days.
An employee of a playschool located in west Delhi's Rohini area was Thursday arrested for sexually assaulting a two-and-a-half-year-old girl after she identified him.