The film starts off with a man running from a Giganotosaurus, the man who is possibly Max Anderson. As the dinosaur pursues him, he comes to a fissure. He tries to jump over, but fails, and falls.
Trevor Anderson (Brendan Fraser) is a Bostonian volcanologist whose 13-year-old nephew, Sean (Josh Hutcherson), is supposed to spend ten days with him. When Sean’s mother drops him off, she leaves Trevor with a box of items that belonged to Max, Trevor’s brother and Sean’s father, who disappeared 10 years before. Sean suddenly takes interest in what Trevor has to say after he tells him about his father, whom he never really had a chance to know. Among the items in the box is the novel A Journey to the Center of the Earth by Jules Verne. Inside the book, Trevor finds notes written by his late brother. At Trevor’s laboratory, the two learn there is a new dot on his radar device on Snæfell, an extinct volcano in Iceland. Trevor goes to Iceland to investigate, and Sean goes with him.
They start by looking for another volcanologist named Sigurbjörn Ásgeirsson and instead find his daughter Hannah Ásgeirsson, the scientist having died years earlier. It turns out that he and Trevor’s brother Max were Vernians, a small group who believe the works of Jules Verne to be fact. Hannah offers to help them climb up to the radar device.
While hiking the mountain, a lightning storm forces the three into a cave that collapses, leaving them trapped. They find it is an abandoned mine. They venture further into the mine, eventually reaching the bottom of a volcanic tube which is full of precious gems. As they are admiring the gems they realize the floor they’re standing on is actually muscovite, a very thin layer of rock formation. The muscovite breaks, and the group falls through the volcanic tube towards the center of the earth, surviving only because the volcanic tube eventually turns into something like a “water slide” which drops them into a lake. There, they find that the center of the Earth is actually another world contained within the Earth.
The group continues seeking a way back to the surface. Along the way, they find evidence that someone was there 100 years previous. Trevor remarks that the instruments found are Lindenbrook’s (a character from the book), hinting that his views of the events of the book being real are changing. They find some of Max’s things as well, such as his water bottle and his journal. While Trevor and Sean are going through what they’ve found, Hannah wanders off and unfortunately discovers Max’s body.
They bury him on the beach of the underground ocean and Trevor reads a letter to Sean found in Max’s journal about how it was Sean’s birthday that day and how Max thought he would never be there to give his son his first baseball glove. They then say their goodbyes and hug each other. Trevor also discovers that his brother died due to dehydration because of the Magma surrounding the center of the Earth.
Using Max’s advice from his journal, Trevor figures that they must find a geyser that can send them to the surface, which is located on the other side of the underground ocean, or else the temperature will rise up to 200 °F, making it impossible to survive. They must reach the geyser in 48 hours or all of the water to create the geyser will have evaporated. They build a raft and begin crossing the underground ocean, but soon encounter prehistoric piranha fish (resembling Xiphactinus), so they use makeshift baseball bats to bat them away, until the arrival of a shoal of Elasmosaurus. After the fish attack, the raft’s sail becomes loose, and Sean tries to hold on, but is blown away and becomes separated from the two adults.
Sean’s guide is now a little bird who has been present since the trio entered the center, and it takes him towards the river. He then goes walking, but then trips and finds out he is in a magnetic field. After he goes through a path of floating magnetic rocks. He almost falls down but was able to hang on. Meanwhile, Trevor and Hannah decide to split up to find him. Sean wanders to find a dry bonefilled land. He hears roars and hides behind a rock. Drool falls next to him, and Sean looks up. He then encounters a Giganotosaurus which drools on top of him and his face. The Giganotosaurus then goes after him. Sean runs away very fast, but the dinosaur is faster. It finds Sean and he yells and cries for desperate help. Trevor – who has desperately been searching for him – finds him. The beast pursues them until they discover that the ground beneath them is muscovite, the same type as earlier. The dinosaur falls through the muscovite, creates a massive hole and dies in the process. They get to a river and find Hannah, using a Giganotosaurus skull as a boat. They sail until they end up at a volcano with magma rising. Then, they feel cold water on the other side of a magnesium wall.
Trevor uses a flare to ignite the magnesium in the wall and causes a geyser to shoot them through Mount Vesuvius in Italy. When they destroy the vineyard of an Italian man, Sean gives him a diamond that he found earlier to say sorry. Trevor sees that he has many more in his backpack, and he uses them to fund his brother’s laboratory. Throughout the adventure, Hannah and Trevor gradually become close and even share a kiss. Sean visits Trevor and Hannah in their new home, which was purchased with some of the diamonds Sean took from the cave. Trevor hands Sean a copy of the book Atlantis: The Antediluvian World by Ignatius L. Donnelly, suggesting they could maybe hang out during Sean’s Christmas break, alluding to a possible sequel. Sean then reveals that he has brought the little bird back from the center of the Earth to keep as a pet. Despite Sean’s entreaties the bird flies away into the screen to effectively end the movie.