The couple - who met on the set of 2012 movie "Her" - are to team up for another film, which will be directed by Lynne Ramsay.
According to El Espanol, Ramsay confirmed the pair are both attached to the project, but plot details are yet to be revealed.
The filmmaker also admitted it was "impossible" not to be excited about working with Phoenix again.
Speaking at the Valencia International Film Festival - which is also known as Cinema Jove - she said, "He's the best actor I've ever met. Everything he does on the set has a reason."
"It's much more difficult when you come up with an original idea like this, but it's impossible not to get excited when you're preparing a movie with Joaquin."
Phoenix and Ramsay worked together on 2017 thriller movie "You Were Never Really Here", in which he portrayed mercenary Joe and she directed the motion picture.
The pair have a baby boy River - who was named after the "Joker" actor's late brother, who died in 1993 - and Mara recently admitted motherhood has made her "more determined than ever" to help create a "kinder and more sustainable world."