In 1821 spirited orphan Mary Yellan goes to live with her aunt Patience at the remote Jamaica Inn on Bodmin Moor, run by Patience's forbidding husband Joss. Since her father was killed by smugglers Mary is not happy to discover that Joss has made the inn the meeting point for a local smuggling gang. Joss's younger brother Jem gives Mary a horse and, although Jem warns Joss to suspend activities because a new magistrate is clamping down on smugglers, Joss ignores him and some of his men are caught. Mary reluctantly helps the gang to clear contraband from the beach before the revenue men can discover it and later sees Joss apparently kill the man who betrayed the smugglers. She is about to go to the law but falls into a bog on the moor, from which she is rescued by Jem.

Mary lies to the magistrate about the inn's involvement with smuggling but feels guilty and visits the vicar, Francis Davey, and his sister Hannah, who partially condone some of the smuggling but disapprove of Joss and ask Mary to spy on him so he can be arrested. Returning to Jamaica Inn she hears Patience argue with Joss about the real smugglers' leader, who gives him his orders. She follows him but gets lost and is again rescued by Jem, who is living rough. After Jem has returned her home a drunken Joss confesses to her that he has nightmares about the sailors he killed for contraband and that her father was also a smuggler, who was hanged. Mary again seeks solace with Jem and they go to an auction to sell the horse - stolen from the magistrate - which he gave her. They decide to spend a night together at a hotel but Jem disappears and Mary is taken home by Francis and Hannah, who are dispensing alms in the area. Francis tells Mary that he has informed the magistrate of Joss's latest plan.

To Mary's horror the wreckers lure a ship onto the rocks and then murder and rob the crew as they swim ashore. However the revenue officers arrive and shoot and kill most of the smugglers, Joss and Mary escaping back to the inn. Joss and Patience decide to flee over the river to Devon but before they can do so both are also murdered. Jem, arrested at the auction for horse-stealing, is released from prison on condition he leads the magistrate to the man who gives the smugglers their orders but Mary, discovering the bodies of Patience and Joss, runs to the Daveys, who are sympathetic and give her tea. However all is not what is seems and Jem must race against time to save Mary and unmask the chief smuggler.