Jolie will direct the drama for Universal Pictures, and the real life couple will produce the movie.
The pair last appeared onscreen together in 2005's Mr. & Mrs. Smith.
It is believed the new film will be shot on location on the Maltese islands of Malta and Gozo.
The actress/director confirmed the news on Friday (18Jul14), stating, "I am very happy to continue my relationship with the entire Universal team as I finish (current film project) Unbroken and begin work on By the Sea. They have created a very special place for storytellers, and I look forward to the continued passion and support they have provided to me as a filmmaker."
Jolie's Unbroken, which chronicles the life of Olympian and World War Two hero Louis Zamperini, will be released in December (14).