In Elk River, Minnesota, sixteen year old high-schooler Juno MacGuff discovers she is pregnant by her friend and longtime admirer Paulie Bleeker. She considers an abortion, until going to a local women's clinic where she encounters a schoolmate outside who is holding a one-person anti-abortion vigil. Once inside, Juno decides to give the baby up for adoption. With the help of her friend Leah, Juno searches the ads in the Pennysaver and finds a childless married couple she feels will provide a suitable home. She tells her father Mac and stepmother Bren, who offer their support. With Mac, Juno meets the couple, Mark and Vanessa Loring, in their expensive Saint Cloud home, and agrees to a closed adoption.
Juno visits Mark a few times, and finds they share tastes in punk rock and horror films. Mark, who has set aside his rock band youth (now confined to memorabilia displayed in the one room of the house that Vanessa has designated for Mark's personal belongings), works at home composing commercial jingles. Juno and Leah happen to see Vanessa in a shopping mall being completely at ease with a child, and Juno encourages Vanessa to talk to the baby in Juno's womb, which kicks for Vanessa.
As the pregnancy progresses, Juno struggles with the emotions she feels for the baby's father Paulie. Juno maintains an outwardly indifferent attitude toward Paulie, but when she learns Paulie has asked another girl to the upcoming prom, she confronts him in a jealous rage. Paulie reminds Juno that it is at her request they remain distant and tells her she broke his heart.
Not long before her baby is due, Juno is again visiting Mark when their interaction becomes emotional. Mark tells her he will be leaving Vanessa to figure his life out. Juno is horrified by this revelation, with Mark asking Juno, "How do you think of me?", revealing he is starting to develop feelings for her. Vanessa arrives home, and Mark tells Vanessa he does not feel ready to be a father. Juno drives away and breaks down in tears by the side of the road. Returning to the Lorings' house, Juno leaves a note and disappears as the Lorings answer the door.
After a heartfelt discussion with her father, Juno accepts that she loves Paulie. Juno then tells Paulie she loves him, and Paulie's actions make it clear her feelings are very much reciprocated. Not long after, Juno goes into labor and is rushed to the hospital, where she gives birth to a baby boy. She had deliberately not told Paulie because of his track meet. Seeing her missing from the stands, Paulie rushes to the hospital, finds Juno has given birth to their son, and comforts Juno as she cries.
Vanessa comes to the hospital, where she joyfully claims the newborn boy as a single adoptive mother. On the wall in the baby's new nursery, Vanessa has framed Juno's note, which reads: "Vanessa: If you're still in, I'm still in. —Juno." The film ends in the summertime with Juno and Paulie playing guitar and singing together, in a happy relationship.
