Jay Wicek attacked the child at a property in Grangemouth, Stirlingshire last year.
The youngster eventually told her mother, sparking a police investigation. It led to Wicek admitting at the High Court in Glasgow to raping the child between March and May last year, although he has since denied the charge.
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Judge Lady Rae told the 16-year-old, of Camelon, Stirlingshire: "I note that you now deny that serious charge despite having sat through the agreed narrative despite having signed the plea. I have, however, as has been accepted by your counsel, no option but to sentence you on this indictment as it stands."
Defence counsel Geoffrey Forbes said the teenager's upbringing was "chaotic" and he had shown remorse.