It’s 1867, and Charles Smithson and Ernestina Freeman are engaged to be married. Charles is an upper-class amateur paleontologist, and Ernestina is the daughter of a rich draper. They’re walking on the shore of Lyme Regis one day when they see a strange woman staring out at the sea. Supposedly she fell in love with a French lieutenant, and she’s waiting for him to return.
The wealthy and religious Mrs. Poulteney hired the French Lieutenant’s Woman, Sarah Woodruff, as a companion a year before. Mrs. Poulteney is an awful woman who’s afraid of hell, so she hopes that her charity towards Sarah will save her own soul. She knows that Sarah helped nurse a French lieutenant back to health when he was shipwrecked, and though Sarah thought he would marry her, he disappeared. Sarah has been an outcast ever since.
Soon after he sees Sarah by the shore, Charles goes out to look for fossils. He ends up in a strange wilderness called the Undercliff, and he comes upon Sarah sleeping in the grass. She wakes and sees him watching her. Sarah often walks in the Undercliff, even though Mrs. Poulteney forbade it because the area is associated with immoral activities. Sarah has continued to walk there, but now she takes extra precautions not to be seen.
The next day, Charles, Ernestina, and Ernestina’s aunt, Mrs. Tranter, visit Mrs. Poulteney and see Sarah at her house. Meanwhile, Charles’s manservant, Sam, is falling in love with Mrs. Tranter’s maid, Mary.
A few days later, Charles goes fossil hunting in the Undercliff again and runs into Sarah. He tells her that he thinks she’s a good person, and Mrs. Tranter would like to help her. Sarah reveals that the French lieutenant has married someone else and he will not be returning for her. Charles doesn’t tell Ernestina or Mrs. Tranter that he’s seen Sarah, and he realizes that he’s attracted to her.
The next time that Charles goes to the Undercliff, Sarah takes him by surprise and says she wants to tell him the story of what happened with the French lieutenant. She feels like she’ll go mad if she can’t talk to someone sympathetic. Charles insists they should stop meeting because it’s not proper, but he eventually agrees that to meet her soon to hear her story.
That evening, Charles, Ernestina, and Mrs. Tranter eat dinner with Dr. Grogan. Afterwards, Charles and the doctor have a drink and begin discussing Sarah. Grogan says she has a bad case of melancholia, and can only be cured if she tells someone her story. They discover that they both believe in the theories of Charles Darwin.
Charles meets Sarah again, and she tells him that she fell in love with the Frenchman, Varguennes, and she slept with him in an inn even though she could tell that he would never keep his promise to marry her. She did it because she feels that the circumstances of her life will never allow her to be happy, and she wanted to be an outcast so that people would recognize her suffering. Later, she and Charles come upon Sam and Mary kissing. As Sarah walks back to Lyme alone, she makes sure that Mrs. Poulteney’s cruel housekeeper, Mrs. Fairley, sees her.
That same day, Charles’s bachelor uncle, Sir Robert, summons him to his estate, Winsyatt. Charles believes that Sir Robert is going to give him the estate, but Sir Robert actually announces that he’s getting married. If he has a son, Charles will no longer inherit Winsyatt or his uncle’s title of baronet.
When Charles returns to Lyme with the bad news, Ernestina is outraged. Charles then learns that Mrs. Poulteney has fired Sarah for walking in the Undercliff and Sarah has disappeared, though Charles finds that she’s sent him a note asking him to meet her once again. Meanwhile, Sam is beginning to realize that something’s amiss, and he’s considering blackmailing Charles so that he can fulfill his dream of starting a shop with Mary.
Charles goes to see Dr. Grogan and tells him about his meetings with Sarah and the note she’s sent him. They’re both worried she might try to commit suicide. Grogan believes Sarah wanted to get fired, and he thinks that she’s so desperate to manipulate people that she might hurt herself in the process. Grogan says he’ll meet Sarah in Charles’s place and take her to an asylum where she can recover.
Grogan gives Charles an account of a strange trial in which a man was convicted for threatening a family and attempting to rape a girl, when in truth the girl just made it seem as though he had committed the crimes. There are also cases of women wounding themselves in gruesome ways in order to manipulate those around them. Though Charles is horrified, he decides that Grogan’s view of Sarah is wrong.
Charles meets Sarah at a barn in the Undercliff. She admits that she let Mrs. Fairley see her walking in the Undercliff so she would get fired, and she says she loves Charles. They kiss, but then Charles rushes out of the barn and finds Sam and Mary outside. Charles makes them promise not to say anything and makes Sarah agree to leave Lyme and go to Exeter.
That day, Charles goes to London against Ernestina’s wishes to inform her father that he may no longer be his uncle’s heir. Mr. Freeman ultimately agrees to let the marriage happen anyway, and he suggests that Charles might one day take over his business, even though gentlemen don’t usually work in trade. Charles feels he can’t refuse, but he begins to loathe his future.
Charles goes to his club and runs into some wild friends he had at Cambridge. They all get drunk and then go to a brothel. Though Charles leaves rather than engage a prostitute, he sees a prostitute on his way home who vaguely reminds him of Sarah, and he hires her. However, he begins to feel ill in her flat. As they’re about to have sex, he discovers that her name is Sarah, and he vomits. She’s very kind to him, and when she goes to get him a cab, he comforts her crying baby.
The next morning, Charles receives a note from Sarah that contains only the name of the hotel where she’s staying in Exeter. Sam reveals his dream to start a shop and makes it clear that he’d like Charles to give him the money. Charles eventually says he’d be willing to do so after his marriage.
Charles and Sam take the train to Exeter, then return to Lyme. Charles and Ernestina live happily ever after, and Mrs. Poulteney dies and goes to hell. However, the narrator admits that this ending is false; it’s only what Charles wanted to happen.
In reality, when Charles arrives in Exeter, he goes to Sarah’s hotel. She’s hurt her ankle, so he goes up to her room. After initial awkwardness, they’re both filled with desire and have sex with each other. Charles says he’ll marry her, but she protests. When Charles is dressing, he sees blood on his shirt and realizes that Sarah was a virgin—she has lied about Varguennes. He’s shocked and confused, and she makes him leave.
Charles goes to a church, where he realizes that he doesn’t need to worry about the judgment of the dead, and that the purpose of Christianity should be to create a world in which Christ can be uncrucified. He decides to marry Sarah instead of Ernestina.
The next morning, Charles sends Sam to Sarah with a letter telling her that he’s breaking off his engagement to Ernestina. If she’s willing to marry him, she should keep the brooch he’s enclosing, and if not, she should send it back with Sam. Sam brings nothing back. Charles goes to Lyme and tells Ernestina first that he was going to marry her for the wrong reasons, then that he’s in love with someone else. She pleads with him and finally collapses.
Charles fetches Dr. Grogan. When Sam finds out what Charles has done, he quits. After Dr. Grogan tends to Ernestina, he visits Charles and tells him how morally despicable his actions are. He’ll have to spend the rest of his life proving that he made his choice for the right reasons.
Charles returns to Exeter, but when he gets to Sarah’s hotel he finds that she’s gone to London and left no way to contact her. Charles discovers that Sam never delivered his letter. On the train to London the next morning, the narrator sits in Charles’s compartment and tries to figure out what to do with him. The narrator decides that he must show two possible endings.
Charles begins to scour London for Sarah, to no avail. Mr. Freeman and his lawyers force Charles to sign a confession of guilt saying that he had an affair and broke his promise to Ernestina without cause. He becomes depressed and travels Europe for a year and a half, finding joy in nothing. Meanwhile, Sam works in Mr. Freeman’s store and begins to be successful. One day Mary sees Sarah going into a house in Chelsea.
Charles goes to the United States and travels extensively until he receives a telegram that his lawyer has found Sarah. He returns to London and goes to the house where Sarah is living, which is owned by the painter Dante Gabriel Rossetti. Sarah is working as his assistant, and she feels like she belongs for the first time. Charles has come to save her, but she doesn’t want to be saved. To his fury, she tells him they can’t be together, and they argue. Just as Charles is about to leave, Sarah reveals that she’s had his child. There seems to be hope that they’ll be together as a family after all.
However, the narrator also presents a second possible ending. After Charles and Sarah argue, Charles perceives that Sarah is offering the opportunity for them to have a platonic relationship. He refuses, and leaves the house without seeing the child. He begins to realize that life cannot be solved, but is meant to be endured.