The woman's lawyer filed a criminal complaint on Thursday, according to news website ameliarueda.com, which said she is a former Miss Costa Rica, without giving further details.
Arias, 78, had already rejected on Tuesday another allegation of sexual assault made by a peace campaigner.
"I deny categorically the accusations made against me," said Arias, who won the Nobel prize in 1987 for efforts to broker an end to Central America's civil wars.
Psychiatrist and peace campaigner Alexandra Arce von Herold, who filed a complaint with police, alleged he assaulted her at his home in 2014.
She had gone there to enlist his support in a campaign against nuclear weapons.
In a complaint to the Costa Rican newspaper Universidad and to The New York Times, she alleged that at the end of the meeting Arias came up behind her and grabbed her breasts and put his hands up her skirt.
She said she was so traumatized that she gave up her lobbying for the NGO she had been trying to get him to support.
The second incident allegedly took place in 2015, ameliarueda.com said.
But the woman also alleges that when she sought legal advice to file a complaint, three lawyers advised her against accusing Arias, the most influential political figure in Costa Rica.
After Arce von Herold's accusation, though, she decided to try again.
Again she was rebuffed by two lawyers before finding someone to represent her.
"When I saw what happened with the new women and the MeToo movement, I thought that I should be brave because I could see that this was habitual behavior," the former Miss Costa Rica said, according to the website.
She said the assault took place in Arias's house after he contacted her through social media and invited her there to give her a book.
She said he "grabbed" her head and pulled her close to him before "he touched my breasts over my clothes and then gave me a kiss against my will."
Arias served as president from 1986-90 and again from 2006-10.
He is currently the head of a foundation to promote peace and disarmament that bears his name.