In 19th century England, young orphan Jane Eyre (Amelia Clarkson), resides with her wealthy but unloving Aunt Reed (Sally Hawkins), the wife of Jane's late maternal uncle. Jane's cousins taunt and abuse her, and Jane is looked upon with disdain by everyone in the house. After reaching her breaking point and physically attacking her cousin, she is sent to Lowood School where dozens of girls are forced to live a meager and miserable life and are frequently beaten in the name of piety. While there, Jane is befriended by classmate Helen Burns (Freya Parks). Jane is heartbroken when Helen, the only kind person she had ever known, dies of consumption.
Years later, 18-year-old Jane becomes a teacher at Lowood. She finally departs when she finds employment as a governess to a little girl living at Thornfield Hall, a large estate miles away. Upon her arrival, Jane is greeted by the housekeeper, Mrs. Fairfax (Judi Dench) who explains to her that the master of Thornfield Hall, Edward Fairfax Rochester, is rarely at home and has a somewhat gruff demeanor, but is a good-hearted man. Jane begins lessons with her pupil, Adele Varens (Romy Settbon Moore), a French girl whose late mother was affiliated with Rochester (it is insinuated that Adele might be their illegitimate daughter). Jane is happy to be living with good people in a comfortable home at last.
After three months at Thornfield, Jane is sent to post a letter. As she walks through the woods, she is startled by a man on horseback galloping by, who falls and injures his leg. Jane assists the man back onto his horse, not knowing that he was, in fact, Mr. Rochester himself.
That evening, Jane is called in to meet Rochester (Michael Fassbender), who has returned home and is nursing his sore leg. He speaks very bluntly and does not bother to sugar-coat any coarse phrases, but is taken with Jane's forward honesty and insightful observations. Jane is confused but quietly intrigued by his mysterious persona and apparent fearlessness.
Late one night, Jane is woken by a strange laugh from the corridor outside her bedroom door. She goes to the hallway and sees smoke pouring from Mr. Rochester's room.Seeing his bed in flames with he still lying in it, she hurriedly wakes him and assists him in extinguishing the fire. She explains the noise she had heard, and he leaves quickly to address it, without telling her what caused it. When he returns, he solemnly thanks Jane for saving his life, saying that he saw a goodness in her when he first met her.
Rochester leaves abruptly the next morning and is gone for weeks. He returns with several guests, including Blanche Inrgam (Imogen Poots), a beautiful and accomplished young woman from a prominent family. Mrs. Fairfax explains that Blanche is "a great favorite" of Mr. Rochester, and expects that they will soon be engaged. Jane is quietly jealous, and is nervous when Rochester insists on her presence in the drawing room with the guests after dinner. She sits with Adele and is completely ignored by the wealthy guests, who callously joke about their disdain for governesses. Insulted, Jane slips from the room but is followed by Rochester, who notices the tears in her eyes before she retreats upstairs. Immediately afterward, Rochester is visited by an old acquaintance, Richard Mason (Harry Lloyd). Mason's motive for visiting is not revealed, but he is brutally stabbed in the dead of night by an unseen culprit. Rochester sends the guests back to their rooms, and enlists Jane to help aid Mason while they wait for the doctor. The weakened Mason is sent off with the doctor the following morning, and Jane asks who had been the violent attacker. Rochester explains that he cannot tell her. He then speaks cryptically of the woman he loves, who Jane assumes to be Blanche Ingram. It is clear that Rochester is speaking of Jane, but neither one admits to it. Jane is flattered by the attention nonetheless.
Jane receives news that her cousin John Reed, who had been her principal tormentor as a child, had squandered his fortune and committed suicide. The shock had brought on a stroke in Aunt Reed, who is in critical condition and requesting to speak to Jane. Despite her resentment toward her abusive former guardian, Jane travels to her old home to visit her aunt. Mrs. Reed produces a letter, dated three years earlier, from Jane's uncle John Eyre who lived on a wealthy estate in Madeira. He wished to adopt his niece as his own and leave her all his possessions upon his death. Jane, who had always been told that she had no living blood relatives, was not given the letter. Reed had written back, telling John Eyre that Jane had died of typhus at school. Jane finally writes a return letter, assuring her uncle that she is very much alive and is relieved to have a living relative. Though furious at this act of deceit, Jane gives her aunt "full and free forgiveness" and returns to Thornfield. She is greeted amiably by Rochester, to whom she had grown close over the span of her employment. Mrs. Fairfax later tells her that Rochester has dropped hints of marriage, ordering jewels from his bank and singing joyfully around the house. Both women assume he intends to marry Blanche Ingram, and Jane is inwardly distressed. She speaks to Rochester primly, saying that she must leave Thornfield and find another situation before he is married. Rochester finally reveals that he is in love with Jane, not Blanche, and begs the stunned governess to marry him. After the proposal sinks in, an elated Jane accepts.
Mrs. Fairfax, startled by the news, warns Jane to keep her wits about her until the wedding. On the day of their marriage, Rochester is strangely impatient and quickly marches Jane to the church for a private ceremony. Before they can say their vows, they are interrupted by a lawyer and Richard Mason, who insist that the marriage be cancelled as Rochester is already married. Jane is shocked to learn the secret: 15 years earlier, Rochester had been in an arranged marriage to Mason's sister, the beautiful but mentally disturbed Bertha (Valentina Cervi). Over the years, Bertha grew more and more insane and violent. To protect her from the cruel treatment she would receive at an asylum, Rochester concealed his wife in a secret room at Thornfield behind a curtain in his own bedroom. She was looked after by a servant, Mrs. Poole, who had dozed off the night of the fire, which was set by Bertha herself. It was Bertha's crazed laugh that had woken Jane and ultimately saved Rochester's life.
Jane is taken to the secret room at Thornfield, where Bertha attacks Rochester after seeing Jane in a wedding gown. Jane is horrified and shocked. She changes back into her plain dress and meets once more with Rochester, who tearfully begs her forgiveness. Jane is agonized by her decision to leave Thornfield rather than to be with a married man, though she still loves Rochester. In tears, she escapes from the house on foot. After miles of walking, she collapses at a doorstep in the rain and is taken inside by the tenants, St. John Rivers (Jamie Bell) and his two sisters. They nurse the weak and sickly Jane back to health, and she gives her name as "Jane Elliott," saying nothing of her time at Thornfield. Rivers, a young minister, gives Jane a job teaching village girls at a small parish school he had established. Though the pay is low, Jane is given a small cottage of her own and begins to enjoy her work and three new friends despite her dashed hopes of being Rochester's wife.
Rivers visits Jane one night and calmly reveals that he knows her true identity. He delivers the news that her uncle, John Eyre, had died and left his entire estate to Jane as promised. Stunned that she is now worth 20 thousand pounds, Jane insists on sharing her new found wealth with St. John and his sisters. Soon afterward, St. John asks Jane to marry him and accompany him to India for his missionary work. Jane loves him only as a brother, and is put off by his businesslike approach to marriage. She finally resolves to return to Thornfield.
Jane is horrified to see Thornfield Hall reduced to a scorched shell. After meeting with Mrs. Fairfax, Jane is told the story of the most recent fire: It was started by Bertha, whose condition had deteriorated even further. Rochester ensured that all the other inhabitants were safely out of the house, and then returned to the inferno to rescue Bertha who had gone up to the roof. He begged her to come down, but she jumped to her death. Rochester escaped the fire, but was blinded. Jane is heartbroken at the news of his suffering. She finds him sitting outside and quietly approaches, leading to a tearful reunion, with Jane and Rochester overjoyed that they can be together at last.