It is not immediately known what specifically led to MacLaren's departure from the Warner Bros project, said the Hollywood Reporter.
"Given creative differences, Warner Bros. And Michelle MacLaren have decided not to move forward with plans to develop and direct Wonder Woman together," the studio said in a statement.
MacLaren, an experienced TV showrunner and director, was set to make her feature debut with the movie.
She has previously directed episodes of "Breaking Bad", "The Walking Dead", "Game of Thrones" and "Better Call Saul".