The exact cause of his death remains a mystery, and is variously attributed to being killed in action against the Western Xia, illness, falling from his horse, or wounds sustained in hunting or battle. According to The Secret History of the Mongols, Genghis Khan fell from his horse while hunting and died because of the injury. He was already old and tired from his journeys.

After he died, his body was returned to Mongolia and presumably to his birthplace in Khentii Aimag, where many assume he is buried somewhere close to the Onon River and the Burkhan Khaldun mountain (part of the Kentii mountain range). According to legend, the funeral escort killed anyone and anything across their path to conceal where he was finally buried.