Locals said the three-year-old girl went to the house of the accused to play with other children like other days on Friday morning.
The accused tactfully took her to his house and raped her, they said.
Hearing screams, neighbours rushed to the spot and rescued her.
Fazlur Rahman, officer in charge (OC) of Phulbari police station, said the accused was handed over to police after the detention.
A case under 'Women and Children Repression and Prevention Act' was filed against him, he said adding that the accused was sent to jail through a Kurigram court later.
The rape survivor sent to Kurigram Sadar hospital for a medical test, the OC added.