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.