Halifax County Sheriff Wes Tripp said Travis Deon Lynch, 38, was arrested and charged today, following an investigation which began last August.
Tripp said Lynch was familiar with the victim but declined to elaborate.
In a statement the sheriff said the child later disclosed she had been raped multiple times.
Detective L.E. Mann obtained warrants after DNA paternity testing was performed and charged Lynch with three counts of statutory of a 13-year-old child.
A magistrate gave Lynch a $100,000 unsecured bond and a June 6 court date.