The actor will be joining lead Jeremy Renner, Edward Norton and Rachel Weisz in the movie, Deadline reports.
Number Three is a brainwashed assassin who comes up against Renner's character. Director Tony Gilroy originally considered Isaac for the central role in the film.
In February, he was on a shortlist with Michael Fassbender, Paul Dano, Luke Evans, Taylor Kitsch and Benjamin Walker.
Watch Oscar Isaac chat to Digital Spy about being linked to The Bourne Legacy below:
Gilroy has described the character played by Renner as a "new hero" and not a replacement for Matt Damon's Bourne.
The director also described the film as a "stand-alone project" rather than a sequel.
Isaac has previously appeared in Sucker Punch and will next star in Cannes hit Drive, alongside Carey Mulligan and Ryan Gosling.
The actor also recently completed filming on Madonna's feature-length directorial debut W.E. about the American Duchess of Windsor, Wallis Simpson.
Watch the new red-band trailer for Drive below: