The novel opens in the small village of Marygreen, where the schoolmaster Phillotson leaves for the city of Christminster with a plan to take a degree and be ordained. He confides this dream to a boy named Jude Fawley, who is left behind drawing water at the village well, already feeling the pricks of life before his time. Jude fixes on Christminster as a city of light and resolves to follow. He teaches himself Latin and Greek from old grammars, expecting language to work like a secret cipher, and is disillusioned to learn how long and hard the real labor will be.
Before he can act on the dream, Jude is trapped. The coarse, lively Arabella Donn sets out to catch him, and after she claims to be pregnant he marries her. The marriage is loveless and short; Arabella eventually leaves for Australia. Jude goes at last to Christminster and works there as a stonemason, repairing the very colleges he may not enter. He writes to the heads of several colleges asking how a poor man might study, and the one reply he gets, from the master of Biblioll College, tells him plainly to stick to his trade. The dream of scholarship is finished.
The emotional center of the book is Jude's love for his cousin Sue Bridehead, intelligent, restless, and contemptuous of convention. To Jude's pain she marries Phillotson, his old mentor, then finds the marriage unbearable and leaves him for Jude. Both eventually obtain divorces, yet Sue refuses to remarry, fearing that a legal vow would poison their love by turning it into an obligation. They live together unmarried and have children, joined by Jude's son from Arabella, a solemn boy nicknamed Little Father Time who seems to carry the sorrow of the world.
Living outside marriage, the couple meet suspicion and are driven from lodging to lodging. The strain of poverty and disgrace presses on them, and on the watchful child most of all. In a single catastrophic scene the eldest boy kills the younger children and himself, leaving a note that reads, Done because we are too menny. Sue's nerve breaks completely. Convinced she is being punished and that she sinned by leaving her lawful husband, she turns back to religion and self-renunciation, and against her own feeling remarries Phillotson.
Jude is left without the dream and without Sue. Arabella maneuvers him into marrying her a second time, and he sinks. Returning to Christminster during the festive Remembrance Week, ill and despairing, he reflects that his and Sue's ideas were simply too early for the world to bear. He dies alone in his room while cheers and music drift in from the river celebrations outside. Hardy closes on Arabella at the festivities and on the verdict that Sue, for all her vows, has not found and will never find peace. The tragedy of unfulfilled aims, as Hardy calls it in his preface, is complete.