The 48-year-old actor is accused of attacking the 51-year-old at his home in New South Wales last month.
He was arrested last Tuesday (1 March) and faces nine offences including having sexual intercourse without consent, and assault with an act of indecency.
According to the Sydney Morning Herald, the charges also include four counts of assault occasioning actual bodily harm and three counts of common assault.
Mr Lynes strenuously denies the allegations and told the Daily Telegraph he would be fighting the charges.
He was granted conditional bail and has been ordered to face Wyong Local Court again on 27 April.
Lynes, who now works in real estate, starred as Adam Sharpe in the long-running Australian soap between 2012 and 2014.
He also played the role of Luke Forlano in Aussie medical drama 'All Saints'.