Gomez-Rejon was among the creative contributors named in the Golden Globe Award for Best Miniseries or Television Film nomination at the 71st Golden Globe Awards for American Horror Story: Coven as Co-Executive Producer/Director. His role as a producing Director meant he had a more regular dialogue with Murphy because he was a creative contributor to all episodes whereas when he had been an episodic Director, he had only been involved in the episodes that he shot. He also worked more closely with the showrunner on casting decisions. He was nominated for an Primetime Emmy at the 66th Primetime Emmy Awards for Primetime Emmy Award for Outstanding Directing for a Miniseries, Movie or a Dramatic Special for his work directing the American Horror Story: Coven episode "Bitchcraft". He is also credited with a nomination for Primetime Emmy Award for Outstanding Miniseries since he served as Co-Executive Producer of the series.
Eventually Murphy sought Gomez-Rejon to direct Glee, where earned his first episodic television directorial credits for executive producers Murphy, Brad Falchuk, and Dante Di Loreto. He credits Murphy for nurturing his early development. In season 1, he directed "Laryngitis" (episode 18, May 11, 2010). In season 2, he directed "Grilled Cheesus" (episode 3, October 5, 2010), "A Very Glee Christmas" (episode 10, December 7, 2010) and "Born This Way" (episode 18, April 26, 2011). In season 3, he directed "Asian F" (episode 3, October 4, 2011).
A new show by Murphy, Falchuk and Di Loreto as executive producers, American Horror Story, debuted in October 2011, and Gomez-Rejon has directed two episodes from the first season: "Home Invasion" (episode 2, October 12, 2011) and "Birth" (episode 11, December 14, 2011). Rejon later returned for the second and third season.
Me and Earl and the Dying Girl, which he directed, was a selection for the U.S. Dramatic Competition at the 2015 Sundance Film Festival. It won the award as well as the US drama audience prize.