In the future, while Elroy is busy working on a time machine, George Jetson comes to Mr. Spacely's office for a serious discussion. Spacely's rival, Cogswell, has been stealing Spacely's business ideas - putting their jobs in jeopardy. Spacely blames George - suspecting that he was spying for Cogswell. Spacely orders George to spy on Cogswell to clear his name to avoid getting fired. George finds out that Cogswell's robot computer, S.A.R.A., has been seducing the Spacely robot computer, R.U.D.I., into leaking Mr. Spacely's secrets. George tries to report this to Spacely, but R.U.D.I. sabotages his efforts.
In the Stone Age, Wilma and Betty are trying to convince Fred Flintstone to have their vacation in Honolurock (Honolulu), but Fred ignores their advances. Later, at work, Fred tells Barney Rubble that he plans to take the girls someplace better. He tells Barney that a poker tournament is being held at the Water Buffalo lodge and wants to go, but Mr. Slate shows up and tells them that due to them going on vacation, they must work the late shift because Turk Tarpit, Slate's business rival and nemesis, has been outproducing them. Fred and Barney later disobey Slate's orders and go to the poker tournament. However, after seeing that Slate is playing there too, they disguise themselves. Fred plays against Slate but loses. A spider exposes Barney - and ultimately Fred. Furious that they deceived and disobeyed him, Slate fires Fred and Barney.
Back in the future, Elroy completes his time machine. The Jetsons decide to use it to take a trip to the 25th century to relax. Right before Elroy gets the machine working, his dog, Astro, accidentally sets the switch to "Past."
With no job, the Flintstones and Rubbles are forced to settle for a camping holiday. As Fred and Barney set up the tent, the Jetsons arrive from the future. Fred and George eventually communicate, and the families become friends. Fred is amazed by George's futuristic gadgets and decides to use them to help Mr. Slate in a competition at the upcoming company picnic. Fred introduces George to Slate - claiming that George is a distant cousin. Slate is reluctant at first to trust George, but since rival businessman Turk Tarpit's cheating has set him back, Slate accepts their help in exchange for giving them their jobs back. George and Fred use future technology to help Slate win several games, but in the last event, Astro's and Dino's actions causes Tarpit to become the winner. In the end, Slate once again fires Fred and Barney.
While Mr. Spacely continues to vent over his failing business, Henry Orbit and Rosie the Robot Maid assemble a "time machine retriever" to bring the Jetsons back. But when they turn it on, the time machine returns with the Flintstones instead. Upon seeing they really are cavemen, Spacely introduces them to the press.
Stuck in the past, George asks Mr. Slate for a job. Slate initially rejects, but when Tarpit offers George work, Slate immediately makes George his partner, and George soon becomes famous. Using their newfound fame and riches, the Jetsons buy multiple local businesses and are soon overwhelmed. Meanwhile, Mr. Spacely makes Fred the spokesman for his company, but R.U.D.I. leaks this information to S.A.R.A. When Spacely is introducing Fred to some important investors, Cogswell introduces Barney instead - leading to a rift in Fred's and Barney's friendship. Meanwhile, Rosie requests R.U.D.I. to help Henry and her try to fix the time machine to find the Jetsons. S.A.R.A. appears and demands that R.U.D.I. get rid of Rosie before she departs, but R.U.D.I. agrees to do whatever he can to get the Jetsons back and leaves S.A.R.A. for good. They fix the time machine, and Rosie is transported to the Stone Age where she finds her family.
Now able to return home, the Jetsons leave, taking Fred's car with them, after Judy says goodbye to a teen idol - Iggy. Mr. Spacely concocts a plan to use Fred's car as a model for futuristic replicas. Cogswell sends his robotic dog, Sentro, to steal this information since S.A.R.A. is no longer useful when she tells him that R.U.D.I. broke up with her and told her off. The two families manage to stop Sentro - destroying the evidence he had collected. Spacely's business of selling Stone Age style cars becomes successful, and he even agrees to sell one to Cogswell - but not without warning Cogswell that if he copies any part of it, Spacely will sue him and take over his business. Fred and Barney repair their friendship, Spacely lets George keep his job, and George offers his partnership with Mr. Slate to Fred and Barney to give them their jobs back. Just as they are about to leave for home, Elroy tells them the time machine is broken and cannot be repaired. Fortunately, they are able to return to the Stone Age because Fred's car absorbed the time machine's "quadrapotents." The Flintstones and the Rubbles then bid a fond farewell to the Jetsons and are sent back to the Stone Age.
The movie has been released on VHS four times, first by Worldvision Home Video, then by Kid Klassics (using the same cassette as the previous release) in 1987, its parent company, GoodTimes Home Video, in 1989, and by Warner Home Video on July 3, 2001. On June 14, 2011, Warner Archive released The Jetsons Meet the Flintstones on DVD in NTSC picture format with all region encoding, for the very first time as part of their Hanna-Barbera Classics Collection. This is a Manufacture-on-Demand (MOD) release available exclusively through Warner's online store and Amazon.com The movie will be made available on DVD again in The Flintstones: 2 Movies & 5 Specials DVD set, to be released on August 4, 2020.
On August 24, 2017, Boomerang's streaming service added the film to its Video On Demand.
The film itself received a mixed to positive response, garnering a 6.5/10 rating on IMDb.
A 1994 Philips CD-i game with a similar premise called Flintstones/Jetsons Time Warp was released in Europe. "A time machine warps Fred Flintstone into the future and George Jetson into the past!"