Jude decides to follow the path recommended by the clergyman and become a low-ranking clergyman. He receives a letter from Sue saying that she is entering the Training College at Melchester, where there is also a Theological College. He decides to wait until the days are longer to travel to Melchester himself because he will have to find work there. Sue writes that she is desperately lonely and begs him to come at once, so he agrees. Jude arrives and takes Sue to dinner. She mentions that Phillotson might find her a teaching post after she graduates, and Jude expresses his anxiety about the schoolmaster's romantic interest in her. Sue at first dismisses his fears, saying Phillotson is too old, but then she confesses that she has agreed to marry Phillotson in two years, and then they plan to teach jointly at a school in a larger town.
Jude finds work at a cathedral and reads theological books in preparation for his career. He goes for a walk with Sue and they find themselves far out into the countryside. A shepherd invites them to spend the night, saying is too late to go back to Melchester if they do not know the way. The next morning the students at Sue's Training College see that she has not returned, and the administrators decide to punish her. She runs away and arrives, cold and soaked from the rain, at Jude's lodgings. He takes her in and hides her from his landlady. They discuss their education, and Sue tells him about an undergraduate she knew in Christminster. They were friends and shared many ideas, but he wanted to be her lover and she did not love him. He died two or three years later. Jude is struck by Sue's freethinking mentality and calls her "Voltairean" (thinking like the French philosopher Voltaire). As they are leaving, Sue tells Jude that she knows he is in love with her and he is only permitted to like her, not to love her. The next morning she writes a letter saying that he can love her if he chooses. He writes back, but does not receive an answer. He goes to find her, and she tells him she no longer wants to see him because there are rumors about their relationship. However, she apologizes in another note, calling her words rash.
Phillotson asks Jude about Sue's history, and Jude assures him that nothing untoward has happened between them. Jude tells Sue his own story, including his marriage to Arabella. She is angered by his previous dishonesty. Two days later he receives a letter saying that Sue and Phillotson are to be married in three or four weeks. Sue also asks if Jude will give her away at the wedding, and he agrees. She comes to Melchester ten days before the wedding and stays in Jude's house. Sue and Phillotson marry on the appointed day. Jude finds he can no longer stand living in Melchester, and when he receives word that his aunt is dangerously ill, he returns to Marygreen. He writes to Sue encouraging her to come and see Aunt Drusilla before she dies.
In the meantime, Jude goes to Christminster for work. He goes to a pub and sees a familiar face: Arabella's. She tells him that she returned from Australia three months before. Jude misses his train to Alfredston and instead goes to Aldbrickham with Arabella. They spend the night together at an inn. In the morning, she says that she married a hotel manager in Sydney. Jude leaves her and unexpectedly encounters Sue. The two go to see Jude's aunt together, and Sue tells Jude that she made a mistake in marrying Phillotson. Jude takes Sue to the train and asks if he can come visit, but she says no. He devotes himself to his studies and develops an interest in music, and on the way back from a trip to see a church composer, he finds an apology and an invitation to dinner from Sue.
Sue shows herself to be both radical in her intellectual views and conservative in her social practices. She leaves the Training College because she discovers that its rules are intolerably strict, and her supervisors' suspicions are too much for her to bear. She comes to see Jude as a protector, and for this reason is disturbed by the realization that he is in love with her. She wavers back and forth in her protests, sometimes wanting to enter into a romantic relationship with Jude and sometimes believing it to be misguided. When he confesses that he is married, she accuses him of dishonesty, but there is a hint of disappointment in her tone because his marriage only adds a further obstruction to their possible romance. She marries Phillotson in this state of anger and frustration, and Jude feels that he cannot and should not dissuade her.
Jude spends the night with Arabella because he feels it is his legal right, and he wants to ease his longing for Sue. When Arabella tells him that she has married a second time, Jude does not know what to do. He regrets his night with her and is dismayed by the realization that he has committed a form of adultery. Meanwhile, Sue tries to push him away again, then invites him to her home soon after. Sue does not know what she wants, but is slowly coming to the understanding that she finds Phillotson repulsive. She does not admit to loving Jude, but still turns to him to be her protector.