A court has heard a US Navy sailor accused of raping a Darwin woman sent the alleged victim a Facebook message apologising for his actions.

Hugh Patrick Malone, 23, is accused of raping a Darwin woman in his hotel room in September 2013.

In opening submissions in Darwin's Supreme Court, Crown prosecutor Matthew Nathan said the complainant and her two friends had made arrangements to meet a group of sailors including Malone at a Darwin bar.

Mr Nathan said Malone, who was from the visiting Navy transport dock USS Denver, invited the woman back to his hotel room while he collected his belongings.

The court heard he then pulled the woman into his room and started to kiss her roughly.

Mr Nathan said Malone then picked her up, put her on the bed and digitally penetrated her, but stopped when she started to cry.

The court heard on the day following the incident, Malone sent the woman a Facebook message.

Mr Nathan read part of the Facebook exchange in court.

"He says, 'look, I know I cannot ask for your forgiveness, I would like to say I am sorry and I mean that with all my heart, it just that when I first saw you I thought [the complainant] was the most beautiful woman I ever saw in my life, but I thought I couldn't have you and I really want you but I just went to your friend and that was the wrong choice, you're so f***ing hot'."

"It was a dumb thing I did, I am sorry [complainant]," the Facebook exchange read, Mr Nathan told the court.

"She responds 'I don't understand why you did what you did ... regardless of whether you had my friend or not you still forced yourself on to me when I said no'," Mr Nathan read.

Malone 'hooked up' with friend of complainant, court told

Mr Nathan told the jury that when the USS Denver docked, a number of US sailors came into town and visited licensed establishments in Darwin.

He said the complainant and her friends went out to meet some of these sailors, and the complainant began a relationship with one of the sailors in the lead up to the alleged offending.

The court heard that on the day of the offence, the complainant was with her friends when she saw the accused and his friend and made arrangements to meet up with the sailors that night.

Mr Nathan said the women came into town about 8:30pm and met up with the accused and his friend at a Darwin bar, Monsoons.

Malone then "hooked up" with one of the complainants friends at a lodge before returning to the bar, the court heard.

Mr Nathan said Malone then began to pester the complainant for sexual activity and she refused for several reasons, including because she was in a relationship with Malone's friend, and the complainant's friend had already had sex with him.

The court heard Malone "acknowledged defeat" and told the complainant he had to get things from his room to check out because the ship was leaving the next morning.

The complainant then accompanied him back to his room, but had intentions to spend the night with her partner.

Mr Nathan said she went with him and initially stood near the doorway but Malone then shut the door and pulled her inside.

"He then commences to kiss her, she describes it quite roughly and she tells him no," Mr Nathan said.

He alleged Malone picked her up, placed her on the bed and digitally penetrated her.

Malone's defence lawyer Tom Berkley gave a brief opening submission.

"This is a case of regret, not a case of rape," he said.

"The issues in this case are this - what happened in that room, whatever happened, was it by consent?

"What was in the mind of Hugh Malone, when he left Monsoons bar to go to the hotel with [the complainant]?" he said.

"Our case is rather simple, that something happened between them, it was consensual that's why they left the hotel together.

"We will be putting out evidence that she led him out of the hotel hand-in-hand, knowing he had just had sexual intercourse with one of her friends."

Mr Nathan said the Facebook exchange made up an unusual part of the evidence.

The trial is expected to last three or four days.