The 30-year-old is accused of sexually assaulting a woman in Hunter Valley, north of Sydney, on 30 September.
New South Wales Police said he has been bailed pending a court appearance in Burwood on 10 December.
Police said they launched an investigation after receiving reports a woman had been sexually assaulted by a man she met on social media.
The investigation is being led by detectives from the Child Abuse and Sex Crimes Squad.
Hayne is currently a free agent having left the Parramatta Eels at the end of the season.
He helped the Eels reach the 2009 Grand Final, scoring 121 tries in 214 NRL games, and has twice won the Dally M Medal awarded to the NRL's player of the year.
Hayne has played 11 Tests for Australia, helping them to win the 2013 World Cup, but has also represented Fiji, where his father hails from.
He left the Eels to play American football in 2015 with the San Francisco 49ers but returned to Australia the following year.