Nawaraj Rai, 40, allegedly raped the eight-year-old girl at her own Chatara-based house who is niece by relation.
Rapist Rai and his wife have been staying at the child's house since one and half years as their house is under construction.
The victim's mother had gone to Dhankuta, Chhintang when the rapist advanced toward her. According to the victim's mother Rai had already raped her twice in the past while there was nobody at home.
The victim has a 15-year-old brother while her father is abroad for foreign employment.
Despite allegation, Rai has not admitted his crime while investigation is underway into the case, Inspector Ram Bahadur Dhakal told Republica.
The minor has been sent to Dharan-based B.P. Koirala Institute of Health Sciences for health check-up.
Man arrested on charge of raping niece