Officials say the accuser is a 26-year-old woman who claimed she hooked up with Hayne on September 30 in what started as a consensual sexual encounter.
Detectives have now charged the 30-year-old with aggravated sexual assault and inflict actual bodily harm.
The 30-year-old was arrested by members of the NSW Sex Crimes Squad in relation to an investigation of a sexual assault allegation made against the out-of-contract NRL star.
The charge carries a maximum 20-year jail term if Hayne is convicted.
Hayne turned himself in to police on Monday and was released on bail several hours later.
NSW Police said the football star had been granted strict conditional bail to appear at Burwood Local Court on December 10.
Australian media's Nine Network reported the alleged victim had been in touch with Hayne via social media and that he travelled to a house in the Newcastle region of New South Wales and had a sexual encounter.
It is understood the NRL then referred the complaint to the police's child abuse and sex crimes squad, who interviewed the woman last Monday. He left the team after one season, saying he didn't want to learn another playbook when San Francisco hired Chip Kelly.
Police declined to charge Hayne after investigating the allegations but the woman lodged a civil suit.
Hayne now does not have a contract for the 2019 NRL season, with his most recent deal with the Parramatta Eels expiring on October 31.
This article discusses sexual assault.