The novel tells the story of Jude Fawley, who lives in a village in southern England (part of Hardy's fictional county of Wessex), who yearns to be a scholar at "Christminster", a city modelled 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 naïve Jude is seduced by Arabella Donn, 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 Arabella leaves Jude and later emigrates to Australia, where she enters into a bigamous marriage. By this time, Jude has abandoned his classical studies.
After Arabella leaves him, Jude moves to Christminster and supports himself as a mason while studying alone, hoping to be able to enter the university later. There, he meets and falls in love with his free-spirited cousin, Sue Bridehead. But, shortly after this, Jude introduces Sue to his former schoolteacher, Mr. Phillotson, whom she eventually is persuaded to marry, despite the fact that he is some twenty years her senior. However, she soon regrets this, because in addition to being in love with Jude, she is horrified by the notion of sex with her husband. Sue soon asks Phillotson for permission to leave him for Jude, which he grants, once he realizes how unwilling she is to fulfill what he believes are her marital duties to him. Because of this scandal the fact Phillotson willingly allows his wife to leave for another man Phillotson has to give up his career as a schoolmaster.