Kamrul Hoda (45), a mechanic was nabbed from Motipur bus stand while trying to flee on bus, Deputy Superintendent of Police (Muzaffarpur west) Anuj Kumar said.
On the complaint of the rape victim, police have registered a case against him with Motipur police station.
The six-year-old girl fell pray to Hoda while she had gone to field to relieve herself yesterday.
Further investigation is on, Kumar said.
The district had come in news recently when Manoj Kumar, the prime accused in Delhi girl's rape case was arrested from his in-laws home in Chiknouta village.