The novel begins when two boys, Ralph and Piggy, find themselves next to a plane crash site (called the 'scar'), unaware of their surroundings. The boys soon find a conch shell and Piggy suggests that Ralph blows on the conch to call for any others who might be nearby. Their situation soon becomes apparent; there are many British school boys and no adults.

These boys are divided into two main groups: the "big'uns" (several older children) and the 'littluns'. Ralph, one of the "big'uns", holds an "impromptu" election and is voted the chief of the boys, beating another elder boy, Jack (the head of a choir group that also landed on the island). Ralph quickly calls everyone together to work toward two common goals, the first being to have fun and the second to be rescued by creating a constant fire signal, which was to be lit using Piggy's glasses. Some of the boys then go exploring and it is discovered they are on a small island.

For a time things on the island are civil, where all the boys worked toward building shelters, gathering food and water, and keeping the fire going. The one goal which constantly gets sidelined is keeping the signal fire going as some of the boys, the 'hunters', led by Jack, focus their energy on hunting the wild pigs on the island. The children's belief in a "beast" on the island also creates a problem. The children begin to split into two groups, based on the existence of the "beast". Ralph attempts to disprove the existence of the beast while Jack exploits the belief in the beast to encourage his group of 'hunters'.

Jack soon forms a separate tribe from Ralph's. Jack gains defectors from Ralph's tribe by promising them meat, fun, and, most importantly, protection from the "beast". Jack's tribe gradually becomes more savage and they use face paint. Jack and his tribe of 'hunters' eventually murder one of the other boys, Simon, who was mistaken for the "beast". They then raid Ralph's camp, attacking the non-hunters in order to steal Piggy's glasses in order to make a cooking fire.

By this time Ralph's tribe consists of just himself, Piggy, and twins named Sam and Eric. They all go to the rock fort of Jack's tribe to try to get back Piggy's glasses so he can see. In the ensuing confrontation Piggy is killed by a falling rock launched by Roger. Sam and Eric are captured and both become part of Jack's tribe, leaving Ralph by himself.

In the final sequence of the book, Jack and his friend Roger lead the tribe of 'hunters' on a hunt for Ralph, intending to kill him. In order to do this Jack sets the entire island on fire. The fire is so large that it attracts the attention of a nearby warship which comes to the island and rescues the boys. A navy officer lands on the island and his sudden appearance brings the children's fighting to an abrupt halt. When learning of the boys' activities, the officer remarks that he would have expected "better" from British boys.

A dead pilot parachutes down to the island one day. The parachutist landed on the rocks and was his parachute got caught. He is spotted and labeled the "beast from the air" by the little children. In response to this, Jack, Ralph and the others set out to hunt this "beast." While traveling, Jack finds a place that he thinks would be a good place for a fort, so they begin preparation by clearing off the ledge. Eventually, Ralph gets them back on their mission, and they continue on, in search of the "beast."
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The story picks up with Jack and his tribe at their new hideout at Castle Rock. They decide to have yet another hunt and kill a large sow. They cut off the pig's head as a sacrifice for the beast and paint themselves in the pig's blood. Simon, alone in the woods hallucinates and thinks the head is the Lord of the Flies, who proceeds to insult his bravery in regard to the "beastie".

Back on the beach, Jack invites the twins, Sam and Eric, Ralph, Piggy, and the littluns to feast with them. After eating, all succumb to the mass hysteria of the tribal dance and kill Simon, thinking he is the beast. Simon was actually coming to bring news that the "beastie" was a dead parachutist. Now Ralph, Piggy, Samneric, and the littluns remain alone with their huts on the beach.