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In 1841, Solomon Northup is a free African-American man working as a violinist, who lives with his wife, Anne Hampton, and two children in Saratoga Springs, New York. Two men, Brown and Hamilton, offer him a two-week job as a musician if he will travel to Washington, D.C., with them. Once there, they drug Northup and deliver him to a slave pen owned by James Burch.

Northup is shipped to New Orleans along with others who have been captured. A slave trader named Freeman gives Northup the identity of "Platt", a runaway slave from Georgia and sells him to plantation owner William Ford. Northup impresses Ford when he engineers a waterway for transporting logs swiftly and cost-effectively across a swamp, and Ford presents him with a violin in gratitude into which he carves the names of his wife and children.

Ford's carpenter John Tibeats resents Northup and the tensions between them escalate. Tibeats attacks Northup, who defends himself. In retaliation, Tibeats and his friends attempt to lynch Northup, but they are prevented by Ford's overseer, Chapin, though Northup is left in the noose standing on tiptoe for many hours. Ford finally cuts Northup down, but chooses to sell him to planter Edwin Epps to protect him from Tibeats. Northup attempts to explain that he is actually a free man, but Ford states that he "cannot hear this" and responds "he has a debt to pay" on Northup's purchase price.

In contrast to the relatively benevolent Ford, Epps is a sadistic man who believes his right to abuse his slaves is biblically sanctioned. The slaves are beaten if they fail to pick at least 200 pounds (91 kg) of cotton every day. A young female slave named Patsey picks over 500 pounds (230 kg) daily, and is praised lavishly by Epps. Epps is attracted to Patsey and repeatedly rapes her, causing Epps' wife to become jealous and frequently humiliate and degrade Patsey. Patsey's only comfort is visiting Mistress Shaw, a former slave whose owner fell in love with her and elevated her to Mistress. Patsey wishes to die and begs Northup to kill her but he refuses.

Some time later, an outbreak of cotton worm befalls Epps' plantation. Unable to work his fields, he leases his slaves to a neighboring plantation for the season. While there, Northup gains the favor of the plantation's owner, Judge Turner, who allows him to play the fiddle at a neighbor's wedding anniversary celebration, and to keep his earnings. When Northup returns to Epps, he attempts to use the money to pay a white field hand and former overseer, Armsby, to mail a letter to Northup's friends in New York state. Armsby agrees to deliver the letter, and accepts all Northup's saved money, but betrays him to Epps. Northup is narrowly able to convince Epps that Armsby is lying and avoids punishment. Northup tearfully burns the letter, his only hope of freedom.

Northup begins working on the construction of a gazebo with a Canadian laborer named Bass. Bass is unsettled by the brutal way that Epps treats his slaves and expresses his opposition to slavery, earning Epps' enmity. One day, Epps becomes enraged after discovering Patsey missing from the plantation. When she returns, she reveals she was gone to get a bar of soap from Mistress Shaw, as a result of being forbidden soap by Mary Epps. Epps does not believe her and orders her flogged. Encouraged by his wife, Epps forces Northup to flog Patsey to avoid doing it himself. Northup reluctantly obeys, but Epps eventually takes the whip away from Northup, savagely lashing Patsey.

Northup purposely destroys his violin, and while continuing to work on the gazebo, Northup confides his kidnapping to Bass. Once again, Northup asks for help in getting a letter to Saratoga Springs. Bass, risking his life, agrees to send it.

One day, Northup is called over by the local sheriff, who arrives in a carriage with another man. The sheriff asks Northup a series of questions to confirm his answers match the facts of his life in New York. Northup recognizes the sheriff's companion as C. Parker, a shopkeeper he knew in Saratoga. Parker has come to free him, and the two embrace, though an enraged Epps furiously protests the circumstances and tries to prevent him from leaving. Before Northup can board the coach to leave, Patsey cries out to him, and they embrace in a bittersweet farewell. Knowing that they are in potential danger, at the urging of Parker and the sheriff Northup finishes his tearful goodbye with Patsey and immediately leaves the plantation.

After being enslaved for twelve years, Northup is restored to freedom and returned to his family. As he walks into his home, he sees Anne, Alonzo, Margaret and her husband, who present him with his grandson and namesake, Solomon Northup Staunton. Concluding credits recount the inability of Northup and his legal counsel to prosecute Brown, Hamilton and Burch, as well as the publishing of Northup's 1853 slave narrative memoir Twelve Years a Slave and the mystery surrounding details of his death and burial.