The late nineteenth century. Professor Abner Perry, a leading scientist, oversees the construction of a giant mole, a 'high calibration digging machine' intended to explore beneath the surface of the Earth.

The mole is ready and a large crowd gathers in Wales for the unveiling and demonstration. Perry is assisted by the American David Innes, once his worst student, now his financial backer.

As the celebrations begin, Perry and Innes enter the mole and sit at the control center. They begin the procedure. But something goes wrong and the mole starts to drill downward at incredible speed. As they penetrate layers of ice and hot rock, both Perry and Innes lose consciousness. They awaken and attempt to maneuver the mole upwards but come to a crashing halt.

Innes exits the Mole and discovers a strange and colourful prehistoric landscape. Perry quickly determines that they have not reached the surface, but are rather at the earth's core. As they continue to examine the fauna and to ponder their options, they are attacked by a very large creature resembling a cross between a dinosaur and a parrot.

As they run away from the beast, they are 'saved' and taken prisoners by another group of creatures, the Sagoth - half-human half-pig. Innes and Perry are chained to a group of other humans captured by the Sagoth. One of these 'locals' is Princess Dia, who explains that the Sagoth are the slaves of the Meyhas, a race of telepathic pterodactyls who rule the city of Pellucidar. The Meyhas use their psychic powers to hypnotise the humans before eating them.

A local named Sly, noticing Dia's interest in Innes, tries to reprimand her. Innes punches Sly and through this gesture, according to local culture, stakes his right to Dia. But he must also kill any man who may already have a claim on Dia. As it happens, a dangerous man named The Ugly One does claim Dia as his. Dia, fearing for her life, escapes.

The chained humans are led into the caves of Pellucidar, where they are put to work until the day when they will be offered in sacrifice to the Meyhas. While working in the mines, Innes escapes and finds a path that leads him outside of the caves. There he meets a local named Ra. After an initial physical struggle with Ra, Innes saves the other man from the deadly grasp of a squid-like creature. They become friends and decide that, together, they must stop the Meyhas. They re-enter the caves but Innes is captured and must fight a giant lizard. He manages to kill the beast and takes advantage of the resulting confusion to find Perry and escape once again.

Outside, they find Dia and save her from a flame-throwing dinosaur. They set out towards the camp where Ra and other humans live. There they create a small army, which teaches to use bows and arrows. Innes is found by the Ugly One, who leads him into a fight; Innes is ultimately the victor.

Later, the small army of men enters Pellucidar. One party, led by Ra, heads for the area of the caves where the egg of the Meyhas is kept and protected, while the other, led by Innes, heads for the lair of the Meyhas. Ra manages to destroy the egg but is killed in the process. Innes and his group find and kill the Meyhas. The caves are destroyed.

Pellucidar is now free and the humans can leave in peace. Innes and Perry make their arrangements for the trip back to the surface of the earth. Dia wants to remain on Pellucidar and Innes decides that he must leave. Perry and Innes enter the giant mole and make their way back to the surface of the Earth.