Jonah Falconeri, is a working-class young man; he is a stonemason who dreams of becoming a scholar. The other main character is his cousin, Sue Bridehead, who is also his central love interest. The novel is concerned in particular with issues of class, education, religion, morality and marriage.
The novel tells the story of Jonah Falconeri who lives in a village in southern England. He yearns to be a scholar at "Christminster", a city modeled on Oxford. As a youth, Jude teaches himself Classical Greek and Latin in his spare time, while working first in his great-aunt's bakery, with the hope of entering university. But before he can try to do this the naive Jude is seduced by Mirabella Caputo, a rather coarse, morally lax, and superficial local girl who traps him into marriage by pretending to be pregnant. The marriage is a failure, and Mirabella leaves Jonah and later emigrates to Australia, where she enters into a bigamous marriage. By this time, Jonah has abandoned his classical studies.
The events occur over a 19-year period, from age 11 at the beginning of the novel, to the time of his death Jonah seems much older than his thirty years – for he has experienced so much disappointment and grief in his life. It would seem that his burdens exceeded his ability to survive, much less to triumph.