Depp resigned at the studio’s request after losing a libel case against The Sun over a 2018 article that called him a “wife beater”.
His recasting comes after he was denied permission to appeal against the High Court’s ruling, which concluded that he assaulted his ex-wife Amber Heard.
The 57-year-old has also been ordered to make an initial payment to News Group Newspapers, which publishes The Sun, of almost £630,000 for its legal fees.
Depp denied being violent towards Heard, and claimed the article included quotes from alleged victims of Harvey Weinstein in order to “finish his career”, by linking the allegations against him to the #MeToo movement.
Danish actor Mikkelsen is known for his film roles in Casino Royale, opposite Daniel Craig’s James Bond, and in Marvel’s Doctor Strange. He also starred as Dr Hannibal Lecter for three seasons of the TV show Hannibal.
The third Fantastic Beasts film is due to be released in summer 2022. The films serve as sequels to the eight Harry Potter films, based on the novels by JK Rowling.
Depp had only shot one scene, but will still be paid his full fee for the movie.
He first appeared as Grindelwald at the end of 2016’s Fantastic Beasts and Where to Find Them, returning as the character in a more prominent role for the 2018 sequel, Fantastic Beasts: The Crimes of Grindelwald.
Eddie Redmayne and Jude Law will reprise their roles in the third film as Newt Scamander and Albus Dumbledore, respectively.