Nora Quoirin, 15, had disappeared from the Dusun Resort, not far from Kuala Lumpur, on August 4, a day after checking in for a holiday with her London-based family.
Her family believed the girl, who had learning difficulties, had been abducted but police classified it as a missing person case.
More than 350 people were deployed to hunt through dense jungle, backed by helicopters, drones, sniffer dogs and divers, while traditional shamans conducted rituals in a bid to locate her.
Deputy national police chief Mazlan Mansor said her body was found in a small stream in a ravine about 2.5km from the resort. He said she was naked but declined to say if she had any injuries.
While officially treating it as a missing person case, police had not ruled out other possibilities.
An open window was found in the cottage where the family was staying at the resort. (AFP)