The central theme of the short story "First Confession" is embodied in its title: Jackie must face a rite of passage into human responsibility by learning the rite of Catholic religious confession and must act as a man and confess to his priest his shortcomings and sins. This involves not just an action and an event, it involves theological comprehension of religious and spiritual truths and the metaphysical function of comprehending how external general rules apply to one's self. This theme is supported and deepened by the sibling rivalry and the refusal of adults to see (or respond correctly to) the manipulations and mechanizations of a cruel sibling toward a milder one or weaker one. In conjunction with this O'Connor presents the theme of a loving and sympathetic relationship between mother and son, a relationship saddened by the mother's absence at the Confession event. Finally the mother-son theme is juxtaposed to the theme of the sympathetic compassion--or lack thereof--of a boy's priest and confessor, since O'Connor believed that the right sort of priest could present the greatest influence possible in the parishioners' lives, parishioners such as Jackie.
One of the themes of "First Confession" is the way in which children, subjected to organized religion, feel that their everyday emotions are sinful. Jackie, a seven-year-old boy, detests his grandmother, as he considers her ill-mannered, and he refuses to eat the dinner she prepares and lashes out at his sister, Nora, with a bread-knife. As a result, his father punishes him. Jackie thinks, "God knows, I was heart-scalded. Then, to crown my misfortunes, I had to make my first confession and communion."
Jackie is frightened to go to his first confession because of what he perceives are his unforgivable sins, and his hypocritical sister Nora makes it worse by asking him, "How will you ever think of all your sins?" The priest, however, takes pity on young Jackie after seeing Nora attack him, and Jackie emerges elated from confession and thinks,
Outside, after the shadow of the church, the sunlight was like the roaring of waves on a beach; it dazzled me; and when the frozen silence melted and I heard the screech of trams on the road, my heart soared. I knew now I wouldn't die in the night and come back, leaving marks on my mother's furniture.
The penance the priest gives Jackie is light, and Jackie is relieved that he won't die a painful death for being a sinner.
The story is about children's misconception of their emotions and actions and also about the hypocrisy of some people's approach to religion. Nora, for example, anoints herself as the paragon of religious perfection while she beats and torments her brother, whereas the priest is a sympathetic character who normalizes Jackie's emotions and lets him know that he is not forever damned.