Hayne leaving Ryde Police Station after handing himself in.
The alleged sexual assault occurred on 30 September - this year's NRL grand final night - at a house in the NSW Hunter region.
The alleged victim claimed she was a virgin and was raped after meeting Hayne in a bar.
The pair allegedly had sex at the location and the woman claims she suffered injuries during the encounter.
7News reports Hayne has refused to answer any questions and charges are set to be laid.
Code-hopper Hayne - who returned home in 2016 after an unsuccessful tilt at America's National Football League - already faces a civil lawsuit in the U.S. over allegations of non-consensual intercourse with a woman in 2015.
Hayne had finished his current contract at the Parramatta Eels on October 31, however the club said they were continuing to provide welfare support.
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The woman originally made a complaint to the NRL's Integrity Unit about the incident who referred the woman to the police.
But the 30-year-old cut it fine, arriving at Sydney's Castle Hill Police Station just 30 minutes before his 8pm deadline.
Welfare officers from the Eels are understood to have been in contact with Hayne since the allegations were made and he was understood to have been rattled by the allegations.
The 30-year-old is accused of aggravated sexual assault and inflicting actual bodily harm on the 26-year-old after meeting her on social media.
A two-time Dally M Medallist, Hayne is one of the biggest names in the NRL.
He has played 214 NRL games since his 2006 debut, 191 with the Eels.
Hayne, has denied the USA allegations and will defend proceedings in a trail set for 2020.