Fowler was an animator for the 2003 short film Rockfish and the 2009 film Where the Wild Things Are. In 2004, he wrote, directed, storyboarded, did the art layout, and animated Gopher Broke. He also wrote and animated A Gentleman's Duel. Fowler worked on the CGI movie production for the 2005 video game Shadow the Hedgehog.
Later, he directed Sonic the Hedgehog, a film based on the video game series of the same name. The film was originally set to release in November 2019, but due to widespread criticism toward Sonic's design, it was delayed to February 14, 2020, to change the design. The new design for Sonic was revealed in November 2019, garnering far more positive responses from fans and critics. Fowler directed a sequel to Sonic the Hedgehog titled Sonic the Hedgehog 2, which released on April 8, 2022. He is set to direct a reboot of The Pink Panther, which is in development.[5] He directed the pilot episode and executive-produced the TV series Knuckles, and directed Sonic the Hedgehog 3, which released in December 2024 to positive reception.