A Portrait of the Artist as a Young Man narrates the early life stages of Stephen Dedalus from childhood to adolescence. Throughout the book, we witness Stephen's transformation from a young boy to an 18-year-old who has made up his mind to depart his homeland for Europe, aspiring to pursue a career as an artist.

At the beginning of the book, Stephen is a youthful child, approximately five years old. He is among the youngest pupils at a boys' Jesuit primary school called Clongowes Wood College (not a "college" in the American meaning). A few days earlier, a student named Wells had shoved him into a drainage ditch outside, and as a result, he falls ill. While recuperating in the infirmary, Stephen fantasizes about going home for the Christmas holidays.

The Dedalus family is shown having a Christmas dinner, during which an argument breaks out between Stephen's father and Dante, Stephen's governess, regarding Parnell and the Catholic church. Later, at school, Stephen's teacher, Father Arnall, excuses him from classwork because his glasses are broken. However, when the prefect of studies, Father Dolan, enters the classroom to discipline the students, he singles out Stephen as a "lazy idle little loafer."

Stephen is punished by having his knuckles beaten with a bat, which he considers unjust. The other students encourage him to speak to the rector of the college, which he eventually does. The rector promises to speak to Father Dolan, and Stephen is comforted by the support of his fellow students.

In chapter two, Stephen is depicted as being a few years older than when he was previously introduced in the story. He is now attending Belvedere College, having left Clongowes behind. Stephen has developed an interest in literature and tends to idealize his life based on what he reads.

He attempts to write a love poem to his beloved, but is unable to do so. Stephen is cast in a play at Belvedere, and while outside the theater, he encounters two fellow students, Heron and Wallis, who mock him about his role in the play and make him recite the Confiteor in jest. This experience triggers a memory of a recent incident in which Stephen's English teacher accused him of heresy.

Stephen and his father visit Cork, where his father shows him around the town he grew up in and the school he attended at Stephen's age. After returning to Dublin, Stephen wins a prize in an essay competition, which allows him and his family to enjoy a brief period of luxury. However, once the money is spent, Stephen can be seen wandering through Dublin's red-light districts, fantasizing about prostitutes. The chapter concludes with Stephen's first encounter with a prostitute.

Chapter Three reveals that Stephen has developed a routine of seeking the services of prostitutes. He maintains this lifestyle while going through the motions of attending school and church without any apparent concern for the dishonesty of his actions. However, during a religious retreat with his classmates, a priest's sermon on sin and damnation has a profound impact on Stephen, causing him to feel remorseful. He confesses his sins at a chapel in another part of town and takes communion.

Stephen has made a commitment to serving God and spends a lot of time praying and practicing self-denial. He has given up his previous sinful behavior with prostitutes and has been approached by the director at Belvedere about becoming a priest. While Stephen initially considers the idea, he ultimately decides that priesthood is not the path for him.

Stephen's father is arranging for him, at the age of 16, to attend university. While walking along the seashore, Stephen contemplates poetry and observes a young woman bathing. Although they exchange looks, they do not communicate. Stephen perceives this encounter as a spiritual indication and becomes thrilled at the prospect of dedicating his life to art.

The last section of the book portrays Stephen being in college, where he neglects his studies but is passionate about his emerging concept of beauty. He declines to endorse a political appeal, distancing himself from the political and religious issues of his country. During a conversation with his intimate pal, Cranly, Stephen reveals his intention to leave Ireland for Europe to pursue his artistic aspirations. The novel concludes with a few entries from Stephen's diary, in which he prepares to depart for the continent.