The charge carries a maximum 20-year sentence if Hayne is convicted.
The pair allegedly had sex at the location and the woman claims she suffered injuries during the encounter.
After voluntarily attending Sydney's Ryde police station he was arrested and subsequently charged by police.
It also transpires that the NRL Integrity Unit have been aware of the incident for some time.
Over the weekend, Hayne hired Salim Mehajer's former lawyer Ramy Qutami.
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. He has played 11 Tests for Australia and 23 State of Origins for NSW and scored 121 tries in 214 NRL games.
The alleged incident occurred on September 30 in the NSW Hunter region.
No charges have been laid and Hayne is yet to comment on the allegations.
The code-hopper - who returned home in 2016 after an unsuccessful tilt at America's National Football League - already faces a civil lawsuit in the USA over allegations of non-consensual intercourse with a woman in 2015.
Hayne has made a career for himself playing professional rugby in Australia for the Parramatta Eels, but he briefly left the team in 2015 to pursue a career in the NFL.
The former Parramatta and NSW origin star is now out of contract and the allegations will severely damage his prospects of a new NRL deal.
This article discusses sexual assault.
Hayne spent the night in jail and was charged with aggravated sexual assault-inflicting actual bodily harm after questioning from detectives in the sex crimes squad.