Police said the cricketer, who is in Australia for the T20 World Cup, and the 29-year-old woman first got in contact via a dating app last Sunday.
After a series of texts and calls, they met for a date on Wednesday before going back to the woman's home in Rose Bay.
Police allege it was there Gunathilaka assaulted her multiple times over a period of several hours.
Detectives launched an investigation on Saturday after reports of the alleged assault and early on Sunday morning the 31-year-old batsman was arrested at his hotel on Sussex St.
He was charged with four counts of sexual intercourse without consent and refused bail to appear at Waverley Local Court on Monday.
NSW Sex Crimes Squad commander Jayne Doherty said the woman took a lot of steps to ensure her safety, including communicating with the man for several days before meeting and going for a date in a public place.
"It was just unfortunate. It has nothing to do with meeting on a dating app or anything," she said.
Gunathilaka travelled to Australia with Sri Lanka's T20 World Cup team but didn't play after being ruled out of the competition with a hamstring tear.
The left-handed batsman has played nearly 100 T20 and one-day internationals for Sri Lanka as well as a handful of tests.
Sri Lanka bowed out of the T20 tournament on Saturday night after losing their final match to England.
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