The film starts off at an Air Force base somewhere in Colorado. The Air Force radar detects a UFO, and they send planes up to examine the situation. The pilots discover that it is a rocket carrying two boys and a robotic dog: Jimmy Neutron, Carl Wheezer and Goddard. Jimmy is attempting to launch a communications satellite made out of a toaster, hoping to communicate with an alien species he believes exists somewhere out in the universe, despite his parents Hugh and Judy's protest in talking to strangers.
After Ms. Fowl, the school teacher, lets the classmates have show and tell at Lindbergh Elementary School, Jimmy, Carl, and their friend Sheen spot a poster for an amusement park called "Retroland." However, Jimmy's parents refuse to let him go that night because it is a school night, and as a result Jimmy is forced to go his room for causing a fire with one of his inventions.
Unknown to anyone, the satellite is picked up near the planet Yolkus, home to an alien race called the Yolkians, who commandeer their war ships that look like a fleet of rubber chickens. King Goobot V and his assistant, Ooblar, watch a pre-recorded message from Jimmy, featuring him introducing himself and explaining about life on Earth. Jimmy, Carl and Sheen subsequently choose to sneak out and visit the park advised by Nick Dean, a popular kid.
As the three are at the park, the Yolkians kidnap all the adults in the city, leaving fake notes on the refrigerators to tell the kids that they have gone to Florida for an "extended vacation". Coincidentally, Carl spots a shooting star (actually a Yolkian ship), so he, Jimmy and Sheen wish for no more parents so they can have fun all the time.
The next morning, the kids discover that the parents have all disappeared and celebrate for the whole day. The next day, after hearing a message from his parents that Goddard had recorded while posing as Jimmy last night, Jimmy becomes suspicious of the fact that his parents said that they would see him in the morning despite not being there. He soon discovers what has really happened.
Jimmy organizes the other children in town to build spaceships from the Retroland rides to travel to Yolkus and get their parents back. Eventually, they are captured by Goobot, who tells them that the parents are to be sacrificed to their god, Poultra. He shows the kids Jimmy's video, thanking him for helping him find suitable species for their ritual, before having the children locked up in their cells, with the exception of Goddard, who is taken by Ooblar to the lab, where he will be tortured.
With Jimmy feeling guilty over the fact that his actions led to the Yolkans abducting the parents in the first place, his rival Cindy Vortex convinces him to stand up and think of an escape plan. After breaking out with the help of Goddard, the children (with the exception of Nick, as he turns out not so brave as he previously seemed to be), in accordance with Jimmy's plan, manage to stop the parents from being sacrificed to Poultra the giant chicken.
Everyone escapes aboard a Yolkian ship, but Goobot follows them in his ship at the head of the Yolkian fleet. With the exception of Goobot's ship, all of the Yolkian ships are destroyed when Jimmy baits them into flying too close to Yolkus's sun. Jimmy and Goddard then use an experimental shrink ray to grow to the size of a planet, and blow Goobot's ship into an asteroid: Goobot and Ooblar survive the explosion, and Goobot declares that they have not seen the last of him and vows revenge. Jimmy reconciles with his parents for not understanding strangers, as all the other kids reunite with theirs, and they make it on their way back home.
In a final scene of the film, Jimmy and Carl have breakfast during which Jimmy's parents drink one of his experiments (that causes significant belching), thinking it is real soda and they all laugh out loud.
Jimmy Neutron: Boy Genius was released in theaters on December 21, 2001, by Paramount Pictures.
Jimmy Neutron: Boy Genius was released on VHS and DVD by Paramount Home Entertainment on July 2, 2002. It was re-released on DVD on June 22, 2011 and re-released again on DVD on April 25, 2017.
The film started out as a short called "Johnny Quasar" in 1995 and was shown at SIGGRAPH that same year. It was intended to be a short pilot for a television series. In 1998, a new short with the main character's name changed to "Jimmy Neutron", called "Runaway Rocketboy", was made and pitched to Nickelodeon with the intent of making it into a television series. The pilot was so successful that the producers wanted to make it into a film, due to the evolution of CGI. However, they were concerned that making a feature film before a television series was too risky, so they made and aired short interstitials on Nickelodeon leading up to the feature's release.
Jimmy Neutron: Boy Genius received generally positive reviews from critics and audiences. The film scored a 75% approval rating on Rotten Tomatoes. The critics' consensus read: "What Jimmy Neutron lacks in computer animation, it makes up for in charm and cleverness." According to Metacritic, the film also scored 65/100, indicating "generally favorable reviews". Rita Kempley of Washington Post praised the film, saying that "this little charmer both celebrates and kids the corny conventions of family sitcoms". Nell Minow of Common Sense Media enjoyed the "stylish 3-D computer animation, good characters", giving the film 3 out of 5 stars. Owen Gleiberman of Entertainment Weekly gave this film a B+, calling it "a lickety-split, madly packed, roller-coaster entertainment that might almost have been designed to make you scared of how much smarter your kids are than you". Paul Tatara of CNN.com called the film "the most delightfully original children's film of 2001". Roger Ebert of Chicago Sun-Times gave the film a 3/4 score, saying that "it doesn't have the little in-jokes that make Shrek and Monsters, Inc. fun for grown-ups. But adults who appreciate the art of animation may enjoy the look of the picture".
The film was financially successful, bringing in $13,833,228 on its opening weekend for an average of $4,407 from 3,139 theaters, and ended up with a total of $80,936,232 domestically, and the film did better overseas bringing in $22,056,304 which made a total of $102,992,536 worldwide. It had a budget of roughly $30 million. It is one of only twelve feature films to be released in over 3,000 theaters and still improve on its box office performance in its second weekend, increasing 8.7% from $13,832,786 to $15,035,649.
Jimmy Neutron: Boy Genius was nominated for the first Academy Award for Best Animated Feature, but lost to Shrek (2001), released by DreamWorks. It was the first release from Nickelodeon Movies to receive an Academy Award nomination.
The movie soundtrack was released on November 20, 2001 after the movie was released, by Sony Music Soundtrax, Columbia Records and Nick Records. There is also an untitled track that talks about chimps.
Additionally, a promotional CD containing the score by John Debney was released for Academy Award consideration.
In June 2002, it was reported that Kate Boutilier had made a deal to write a sequel to the film. However, there was not any progress in the project and was cancelled.
An event that aired on May 19, 2007, Nickelodeon rehired the original voice actors of Jimmy, Sheen and Carl to return for a special audio commentary version of the film that features their animated counterparts' silhouettes, spoofing Mystery Science Theater 3000.
These shorts were used to promote the film. They have all been released on the official Jimmy Neutron: Boy Genius DVD release of the film. All of the inventions in each short were seen again at some point on the television series (except for the Pain-Transference helmet). Clips from similar versions of these shorts, along with clips from the unaired "Runaway Rocketboy" pilot, appeared in the teaser trailer for Jimmy Neutron: Boy Genius. The biggest difference between the clips seen in the trailer and the original shorts is that Jimmy wears the white and red striped shirt he wore in the pilot, rather than his trademark shirt.