During the first ice age, a caveman (Brendan Fraser) is seen with his cavewoman girlfriend (Sandra Hess) as he makes a fire, until an earthquake causes a cave-in that buries them.
In the present day, Dave Morgan (Sean Astin) and Stanley "Stoney" Brown (Pauly Shore) are two high school outcasts who strive for popularity.
While digging in Dave's backyard to make a swimming pool, they find a block of ice containing the caveman. While Dave and Stoney are at school, the heaters they are using thaws the caveman and he comes to life. While exploring his surroundings, he encounters Dave's dog, gets into a "battle" with a garbage truck, and ends up dancing to the music of the music video on the television when he steps on the remote.
Upon returning home, Dave and Stoney discover that the ice containing the caveman has melted. When they enter the house, they find cave paintings on the furniture. After hearing the smoke alarm, they follow the footprints to Dave's room where they find the caveman starting a fire. Dave and Stoney enter the room and try to befriend him. When the caveman starts reacting to the telephone and charges at Dave, Stoney soothes him by showing him a lighter.
After a bath, shave, haircut, and new clothes, the caveman is named Link (as in Missing link) by Dave and Stoney who try to pass him off as a regular teenager (as Estonian exchange student Linkavitch Chomofsky). Dave manages to convince his parents to let Link stay with them. After enrolling him in their high school, Link becomes very popular with everyone, ranging from the geeks at the AV Club to the hip hop enthusiasts. As a result, Stoney and Dave begin to acquire their much desired popularity, and Dave begins to rekindle a friendship with his love interest Robyn Sweeney (Megan Ward) who Dave had lost his chance with because she "Hadn't hit babehood yet" prompting her boyfriend Matt Wilson (Michael DeLuise) to become angered with jealousy. Snobbish and conceited, Matt attempts to undermine Link's popularity and in the process helps to block Dave and Robyn's budding romance. Robyn asks Link out to the Prom, much to Dave's chagrin, and Stoney's influence turning Link into a replica of him causes the three of them to go their separate ways. Dave attempts to force Link to leave. Stoney stops him and the two get into a fight, but Link intervenes. The pair apologize and make amends.
Matt, having been defeated by Link in a brawl at an ice rink, which originally prompted Robyn to break up with him, attempts to expose Link for who he truly is by breaking into Dave's house during the Prom. Matt discovers photographs of Dave and Stoney with Link as a caveman, and during the Prom he attempts to expose Link for being a freak. His plan backfires and Link, Stoney and Dave become more popular than ever. They then lead the entire school body in an energetic, caveman-like dance followed by an after-prom party at Dave's house.
While there, Robyn and Dave confess their love for each other, Link and Stoney follow an eerily familiar trail of smoke and paint through Dave's house and discover Link's girlfriend, the cavewoman from the beginning of the film, bathing in a bathtub with bubbles. Link excitedly joins her and the two embrace happily.