Johnston and fellow Mr. Show regulars Dino Stamatopoulos and Scott Adsit, were part of the creative team (voicing, writing, directing and producing) behind Adult Swim's stop-motion animation series Moral Orel, which ran from 2005 to 2008. In 2010, Johnston provided voices for Stamatopoulos' Adult Swim series, Mary Shelley's Frankenhole.
In 2006, Johnston regularly appeared as "The Boss" on FUEL TV's American Misfits, in the show's intro and outro Sketch segments. The show is a half-hour mix of skateboarding and sketches, very much in the mold of the early 1990s skateboarding videos.
Johnston starred on all three seasons of Comedy Central's The Sarah Silverman Program as "Officer Jay McPherson", the love interest of Sarah's sister Laura in the series. The series reunited Johnston with Mr. Show cast members Brian Posehn, Scott Aukerman, B. J. Porter, and Paul F. Tompkins. In 2011, Johnston appeared as a Sketch regular in season two of the Comedy Central Sketch comedy series Nick Swardson's Pretend Time.
