Dougherty was born and raised in Columbus, Ohio and attended the Tisch School of Arts at New York University in the Maurice Kanbar Institute of Film and Television, which is where he produced Season's Greetings (1996). His mother is Vietnamese.
Bryan Singer, Dougherty and Dan Harris provided the plots to four comic book prequels to Superman Returns. The four forty-page comic book prequels were published by DC Comics throughout the month of June 2006 and bridged the gap between the second Superman film and Superman Returns.
His directorial debut, Trick 'r Treat, is based on his own script, and was produced by Bryan Singer. It played at several film festivals, before being released on DVD on October 6, 2009 in the US and Canada. In December 2014, he began work on his horror film Krampus, which was released in December 2015, and co-wrote the script for X-Men: Apocalypse (2016), with Singer, Dan Harris and Simon Kinberg, with Singer once again as Director. In October 2016, it was revealed that Dougherty will write the script for Godzilla: King of the Monsters along with Zach Shields. A day later, it was reported that Dougherty is also in negotiations to direct Godzilla: King of the Monsters. In January 2017, Dougherty was officially announced as the Director for Godzilla: King of the Monsters.
In 2015, with Todd Casey, Zach Shields and Marc Andeyko, Michael Dougherty co wrote and created a comic book tie in to Trick 'r Treat, titled 'Trick 'r Treat: Days of the Dead'. It features four new short stories, spanning centuries, depicting a variety of characters and cultures, going back to the holiday's roots in ancient Ireland.
