Ned Malone, a reporter, is in love with Gladys Hungerton. She has rebuffed his proposal of marriage, because she wants to marry a man who has faced death in the pursuit of a great deed. Ned approaches his editor, McArdle, with the idea of doing a story that will fulfill Gladys's requirement.

McArdle sends Ned to interview Professor George Challenger, who has stated he discovered living dinosaurs in South America. The combative professor has already injured one reporter who has tried to interview him, so Ned knows he must be cunning if he is to gain the man's confidence. To achieve his goal Ned enlists the help of his friend Tarp Henry, a bacteriologist on the staff of Nature. Tarp allows Ned to use his letterhead on a letter to the professor, asking him some questions about a lecture he had given. Ned poses as a student of science, which leads Challenger to agree to see him. It also leads Challenger to the conclusion, after asking Ned some questions, that Ned is in reality a journalist.

After a fistfight, Ned gains Challenger's trust and he asks Ned to see him speak at a lecture of the Zoological Institute. There Challenger tears apart the lecturer's speech and he himself is subjected to ridicule, by some members of the audience. It is because of this, a committee is formed to go to South America and explore Challenger's claims, those who volunteer are Professor Summerlee, Lord John Roxton, and Ned Malone.

Ned and his editor agree that Ned will send back letters about the expedition and after the consent of Challenger, edit them for publication. As the three men are boarding the ship to sail to South America, Challenger comes on board with some final instructions. He tells Ned he may print whatever he wishes about the expedition, as long as he does not give their location, then he hands the men an envelope. He tells them they are to open the envelope, at on certain time and day, in the town of Manaos.

In Manaos the men hire six natives to help them on their journey and they also open the envelope. The envelope contains only a blank piece of paper, but Challenger soon arrives and explains he will accompany them on the trip.

He has hired a boat to transport them down the Amazon River and has also brought two Indian guides along with him. Professor Summerlee, who does not believe Challenger's story, and Challenger bicker the entire journey. As they are walking through the jungle, Challenger sees a winged animal, which he calls a pterodactyl, but Summerlee insists is a stork.

Once the men reach the base of the plateau, which is where the dinosaurs live, they look for a way to scale the cliffs, that surround the plateau. While they are exploring they discover the base camp of Maple White, he is the first discoverer of the plateau. Challenger knew of Maple While, because he had been asked to save his life, but the man was dead by the time he arrived to help him. He did discover in Maple White's pocket a sketch book which detailed where the plateau was and what was on it.

One night, while they are exploring the plateau base, the men roast a pig-like animal for their supper, when out of the sky a large animal swoops down and takes the animal. Professor Summerlee has to admit the animal is a pterodactyl, which allows him and Professor Challenger to become friends.

The men eventually scale a precipice and using a tree as a bridge, they are able to reach the plateau. Their joy is short lived after one of the hired natives purposefully pushes the bridge down and thus strands the men on the plateau. The hired man does this as revenge for his brother's death at the hand of Lord John.

During their explorations, the men come upon a pterodactyl rookery in a volcano pit. They are attacked and escaped, only to find that their camp has been ransacked by an unknown creature. The next night they hear two dinosaurs fight and know one of them has been killed. Professor Summerlee is now insistent that all their energies be directed to finding a way off the island.

The next evening Ned goes for a walk by himself and discovers caves, which have light coming from them. He knows these lights are probably produced by human-like animals. On his return he finds the others gone, because of this he calls to Zambo, the native who has stayed to help the men, and asks for a rope.

The next morning Lord John returns to the camp and explains to Ned how he and the others were captured by ape-men and taken prisoner. The two of them arrive just in time to save Challenger and Summerlee from death. They then join the Accala tribe, whose lights Ned saw, in a fight to rid the plateau of the dangerous ape-men. They are successful and the chief's son helps the four men leave the plateau, so they can return to London.

Once there, the report they give to the Zoological Institute is met with skepticism, until Challenger produces a live pterodactyl for all to see. The men are then treated as conquering heroes, but Ned finds out that Gladys has married another man. They also discover they are rich, because Lord John discovered diamonds on the plateau. He shares the money they are worth with the others.

This book is about a man's desire to prove himself to himself and the world; this is true of Ned and the other three men in the expedition. It is also about being open to believe the unbelievable, such as Challenger asked each of the other three to do. They fight a moral dilemma, because they are a little unsure if they should help in the battle between the Accala and the ape-men.