His first behind-the-scenes work was as writer and producer on the NBC series "Silver Spoons" (1985-86) and "Night Court" (1986-88). After developing an adaptation of the popular British sci-fi comedy "Red Dwarf" for American television that disappointingly didn't get past the pilot stage, Boomer moved on to the relatively short-lived sitcoms "Flying Blind" (Fox, 1992-93) and "The Boys Are Back" (CBS, 1994-95), writing episodes for both and serving as executive consultant of the former and co-executive producer of the latter. In 1996 he was one of the executive producers of the hit NBC sitcom "3rd Rock From the Sun" and the failed ABC entry "Townies". While he also served in the same capacity for the edgy but controversial animated series "God, the Devil and Bob" (NBC, 2000), he found immediate success with the envelope-pushing Fox family comedy "Malcolm in the Middle" (2000- ).
A midseason replacement, "Malcolm" quickly won an audience with its boldly realistic yet off-kilter comedy focused on a struggling middle-class family of six: high-strung disciplinarian mother Lois (Jane Kaczmarek); dim but well-meaning father Hal (Bryan Cranston); smart aleck eldest son Francis (Christopher Masterson) consigned to military school; bullying, reluctant boy genius Malcolm (Frankie Muniz); and just plain weird youngest child Dewey (Erik Per Sullivan). The series steered clear of the traditional sitcom trappings as it was shot in a single-camera style, with no laugh track and with frequent fourth wall-breaking commentary by the title hero. "Malcolm in the Middle" set itself apart from its competitors with a fresh and consistently funny perspective and the remarkable performances by the entire cast. Perhaps this was in part because the show was loosely autobiographical for Boomer. Like Malcolm, he was the second youngest of four boys in a resultingly rowdy household, had a strict mother and was enrolled in a gifted program at school much to his dismay. An opening scene in the series' first episode that featured mom shaving dad's body hair at the breakfast table was said to have been taken from Boomer's own upbringing, and such unabashed displays of decidedly non-sitcom-like behavior impressed viewers and critics alike.