Jude Fawley dreams of studying at the university in Christminster, but his background as an orphan raised by his working-class aunt leads him instead into a career as a stonemason. He is inspired by the ambitions of the town schoolmaster, Richard Phillotson, who left for Christminster when Jude was a child. However, Jude falls in love with a young woman named Arabella, is tricked into marrying her, and cannot leave his home village. When their marriage goes sour and Arabella moves to Australia, Jude resolves to go to Christminster at last. However, he finds that his attempts to enroll at the university are met with little enthusiasm.
Jude meets his cousin Sue Bridehead and tries not to fall in love with her. He arranges for her to work with Phillotson in order to keep her in Christminster, but is disappointed when he discovers that the two are engaged to be married. Once they marry, Jude is not surprised to find that Sue is not happy with her situation. She can no longer tolerate the relationship and leaves her husband to live with Jude.
Both Jude and Sue get divorced, but Sue does not want to remarry. Arabella reveals to Jude that they have a son in Australia, and Jude asks to take him in. Sue and Jude serve as parents to the little boy and have two children of their own. Jude falls ill, and when he recovers, he decides to return to Christminster with his family. They have trouble finding lodging because they are not married, and Jude stays in an inn separate from Sue and the children. At night Sue takes Jude's son out to look for a room, and the little boy decides that they would be better off without so many children. In the morning, Sue goes to Jude's room and eats breakfast with him. They return to the lodging house to find that Jude's son has hanged the other two children and himself. Feeling she has been punished by God for her relationship with Jude, Sue goes back to live with Phillotson, and Jude is tricked into living with Arabella again. Jude dies soon after.