Upon investigation, police discovered the accused male entered the house through an unlocked door.
He physically restrained the woman before forcing her to have sex with him.
The accused is also reported to have kept the woman inside the house against her will for over an hour.
The suspect is a 27-year-old male.
The victim and the accused had been in a relationship, but were estranged at the time the assault was reported to police.
Cpl. Franco Radeschi said no one else was in the house at the time.
The accused is currently in Iqaluit awaiting a show cause hearing.
Radeschi said Kugluktuk has "limited resources" when it comes to dealing with victims of violence.
But the community does have a womens group and a womens shelter, he said.
"Some communities are better off than others," said Radeschi.
"We could use more resources, though. We all can."