The film focuses on 16-year-old Juno who realizes she's pregnant with a child by friend and admirer Paulie. Unwilling to raise a child so young, she looks into abortion but chooses to put the child up for adoption. With some help from Leah, a friend of Juno's, she looks in newspapers ads for couples seeking to adopt. After telling her supportive parents, Juno goes to meet the seeking couple with her father. Juno sees that Mark and Vanessa have an expensive house, meaning they could give plenty of support to the baby; ultimately agreeing to a closed adoption.
Juno visits Mark a few times, curious that he has the same taste in music and horror films, to Vanessa's agitation. While at a shopping mall and noticed Vanessa perfectly at ease with a child, Leah asks Juno to speak to her baby, where it responds with a kick. as the pregnancy goes on, Juno must deal with her emotions over Paulie, who obviously loves her. Outraged upon hearing that he asked a different girl to the prom, Juno confronts him only to be shot down. Paulie reminds her that they promised to remain distant, also sharing with her that she was the one who broke his heart.
With the baby soon to arrive, Juno's visits with Mark become emotional. Mark confesses his desire to leave Vanessa, which horrifies Juno, especially upon his question to her of "How do you think of me?" Vanessa returns home at this moment with Mark explaining to Vanessa that he's not ready for fatherhood, that he has things he still wants to do. Juno sees their marriage shatter, driving away and breaking down in streaming tears. She eventually returns to their home, only leaving a note when the door isn't answered.
After an emotional talk with her father, Juno accepts her love for Paulie. She shares this news with him, who returns the adoration with Juno going into labor soon after. Racing to the hospital, Juno manages to deliver a boy. Although Juno hadn't told Paulie she was about to go into labor, so as not to mess up his track meet, Paulie figures things out when she's not in the stands and rushes to the hospital to see Juno with her son. Vanessa shows up, claiming the newborn boy as a single mother. Vanessa has Juno's note framed in the nursery, stating that if Vanessa still wants a baby, then she can raise the child.