The woman alleges she sustained an injury during the non-consensual encounter in the NSW Hunter Valley region on September 30.
Hayne handed himself in at Ryde Police station where he was placed under arrest before being questioned by detectives from the New South Wales Child Abuse and Sex Crimes Squad.
Hayne is yet to comment on the charge. The investigation ultimately led police to Hayne, who has since been released on bail pending a court appearance on December 10.
According to NSW Criminal Code, a sexual assault becomes "aggravated" if the offender inflicts "actual bodily harm on the alleged victim intentionally".More news: YouTube is making movies available for free in the US
It also transpires that the NRL Integrity Unit have been aware of the incident for some time.
The alleged victim said she and some friends met Hayne and his friends at a bar.
Hayne, a two-time Dally M Medallist, is one of the biggest names in the NRL and had a magical run to help the Eels to the 2009 grand final.
This would mark the second time Hayne has been accused of a sex crime, having been accused back in 2015, when a woman in the U.S. claimed he raped her after she had been drinking and passed out.More news: Police called after Chinese bully host at Pacific summit
Police investigated the incident but decided not to charge Hayne.
Hayne's future in the NRL was already in limbo with the off-contract star yet to be offered a new deal by the Parramatta Eels.
New South Wales Police confirmed that a 30-year-old man had been arrested.More news: Redskins’ QB Alex Smith Suffers Gruesome Leg Injury Vs. Texans