Cornwall, 1819. Joss Merlyn and his gang lure a ship on to the rocks off the coast. As the crew attempt to escape the wreck, they are slaughtered by the gang, who make off with the ship's cargo.

A young Irish woman, Mary Yelland, is travelling by coach, on her way to stay with her aunt at Jamaica Inn. But the driver, who is fearful of the place, refuses to stop at the Inn, instead dropping her off at the estate of Sir Humphrey Pengallan, local squire and Justice of the Peace, who is entertaining guests. Sir Humphrey is impressed with Mary's beauty, and offers to escort her to Jamaica Inn.

There, Mary is greeted by her uncle, the brutish Joss Merlyn, and by her Aunt Patience. She tells her aunt of the death of her mother - Patience's sister - and asks to stay. In the hallway, Mary overhears men's voices from another room, where Joss' gang are gathered.

When Joss learns that Mary was brought to the Inn by Sir Humphrey, he becomes agitated. He goes to an upstairs room, where he finds his employer - Sir Humphrey - waiting. Sir Humphrey complains about the size of the booty. There is a commotion downstairs, and Joss goes to investigate. The gang have turned on Jem Trehearne, the newest member, suspecting him of stealing more than his share. They decide to hang him.

The men leave Jem swinging from a beam, then begin fighting over his possessions. Meanwhile Mary, who has been watching through a gap in the wall, cuts him down and helps him to escape. When Patience learns what she has done, she begs Mary to leave too.

Mary and Jem head for a cave on the coast, with Joss' men in pursuit. The next morning when she awakes, she becomes frightened by Jem and tries to escape in a boat, but he stops her. In the process the boat drifts away. The gang track them down to the cave, but they escape by swimming. At Mary's suggestion, they head for Sir Humphrey's estate, where they ask for his help. Jem privately tells Sir Humphrey that he is an officer of the law.

Back at the Inn, Sir Humphrey and Jem capture Joss and interrogate him about his secret employer. When Jem leaves the room, Sir Humphrey tells Joss about a new job - a ship carrying gold is passing the coast that night. When Jem is overpowered by Joss' gang, Sir Humphrey contrives to be 'captured' by Joss, and the pair are tied up. Patience is instructed to watch them, while Joss and his gang, with Mary in tow, head for the coast to prepare for the shipwreck. When the gang have left, Sir Humphrey releases himself and departs, leaving Patience to watch over Jem who, after promising to let Joss go free, eventually persuades her to release him.

At the coast, Mary sneaks away from the others and tries to raise a light to warn the ship, but she is seen by one of the gang. In the struggle, the lantern starts a fire. The ship escapes, and the men turn on Mary. Joss intervenes to protect her, and is shot as they escape. Mary helps him back to the Inn, where she and Patience try to revive him. Patience tries to tell her about Sir Humphrey, but is shot before she can finish. Immediately after, Joss dies of his injuries.

Sir Humphrey appears, with gun in hand. As he gags and binds her, he tells her he is leaving the country, taking her with him. They are spotted leaving by the returning gang. The gang find Joss and Patience's bodies, and decide to scatter, but before they can leave Jem arrives with troops, and the gang members are rounded up.

Jem learns that Sir Humphrey has taken Mary, and heads off in pursuit. Jem and his troops catch up with them at the docks, where their ship is about to depart. Mary, now convinced Sir Humphrey is insane, begs them not to harm him. When he realises he is cornered, Sir Humphrey climbs the rigging, finally jumping to his death. Jem leads Mary away.