By the end of his stint on "In Living Color", Oedekerk had completed and sold the original screenplay "Nothing to Lose" (1997), a buddy movie that paired Martin Lawrence and Tim Robbins. He also directed and played a bit role in the movie, which did not exactly bowl over critics or audiences. Oedekerk quickly lined up a series of assignments including co-writing the 1996 remake of "The Nutty Professor" as a vehicle for Eddie Murphy. He went on to headline his own 1997 NBC comedy special "steve.oederkerk.com" and wrote the treacly script for the Robin Williams vehicle "Patch Adams" (1998).

In 1999, Oedekerk premiered "Thumb Wars" (UPN), a spoof of George Lucas' "Star Wars" franchise using thumbs dressed as characters. He quickly spun the idea off into an Internet-related site (thumb.com, part of www.ochannel.com). His next project proved to be a winner in many ways. Oedekerk was one of the creative forces behind the animated feature "Jimmy Neutron, Boy Genius" (2001), which became a surprise nominee for the first Best Animated Feature Academy Award. By the time the movie, about an inventive young boy who takes on space aliens to save the world, was opening in theaters, Nickelodeon had already committed to producing a TV series spin-off which premiered in 2002.

A fan of Hong Kong martial arts films, Oedekerk took a page from early Woody Allen and obtained the rights to "Tiger & Crane Fists" (1976) and altered the movie, dubbing all the characters' voices, inserting himself into scenes digitally and filming new material to create "Kung Pow: Enter the Fist!" (2002). The result of recent footage edited into the existing material was amusing to some, dull to others. Later that same year, he served as a producer on the comedy "Juwanna Man".