"Mr Hayne unequivocally and vehemently denies the allegations which are the subject of the civil complaint", he said in a statement.
According to reports, the Santa Clara County DA's office investigated the alleged incident in October, 2016 but did not proceed with a criminal case due to insufficient evidence.
The woman, whose identity is protected in court documents, made the allegation in a civil lawsuit filed against Hayne on Wednesday in Santa Clara County.
High profile United States attorney John Clune is the lawyer preparing to take on Jarryd Hayne in a California court over accusations the NRL star raped a woman during his time with the San Francisco 49ers.
"He then had non-consensual sexual intercourse with her". The woman alleges she was heavily intoxicated when Hayne took her to his home "despite having minimal interaction that night". She was initially hesitant to contact the authorities because she "had heard of many cases, especially involving high profile athletes, where victims were discredited and even blamed" but eventually reported the rape to the San Jose Police Department in May 2016.
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The case was formerly rejected in October a year ago due to insufficient evidence.
A spokesperson for the NRL said the league's Integrity Unit would continue to monitor Hayne's case.
They said they were trying to get in touch with Hayne and his support team as soon as possible.
"As with any legal matter, it is important that we follow due process and ensure that we review all relevant information available, including giving Jarryd the opportunity to respond".
Hayne played one season and eight total games with the 49ers in 2015.
"The Club will continue to monitor the situation and when appropriate we will provide an update to members and media". He is now playing for a professional rugby team in Australia. He announced last month he would be released from his record $1.2 million contract to return to Parramatta for the 2018 season.