16-year-old Juno MacGuff has gotten pregnant after sleeping with Paulie Bleeker in a recliner armchair. She decides that it’s best to have an abortion as she isn’t prepared to have a child, but when she goes to the clinic she can’t do it, after being reminded by a classmate protesting abortion outside that her baby likely has fingernails already. Juno has to tell her dad and stepmom, Bren, what’s happened, and that she has decided to keep the child and give the child up for adoption. Her dad goes with her to meet Mark and Vanessa Loring, who are unable to have kids of their own. Juno really likes them, especially Mark, who is into music and horror films just like her, and is an ex-punk. The film progresses through the seasons of her pregnancy, beginning with Autumn.
As we move through Winter and Spring and Juno's pregnancy begins to show, complications ensue. While she and Bleeker have stayed in contact, they aren’t together anymore. Juno goes to Mark and Vanessa’s home to show them what’s happening after she gets her first ultrasound. The boundary between birth parent and adoptive parent begins to blue as Juno and Mark start to hang out alone at the Loring's house, without Vanessa. Late into her pregnancy, Juno finds out that Bleeker is taking another girl to prom. This upsets her and she berates him for abandoning her. We also find out that Bleeker has actually been heartbroken by Juno since he found out she was pregnant.
In order to get back at Bleeker, Juno heads over to Mark’s house for some male attention. Again, Vanessa isn’t home and she has brought music over for him to listen to. They put it on and it turns out to be the song that Mark danced to at his senior prom in high school. They dance, with Juno resting her head on his shoulder. In this moment of vulnerability and closeness Mark reveals that he is leaving Vanessa. This is shocking to Juno and she storms out of the room. As Juno is leaving Vanessa comes home and sees she’s upset. Mark reveals that he isn’t ready to be a father.
Juno leaves and turns up at home to find her dad working at the kitchen table. She asks him if he believes two people can actually stay together, and though he’s been through a divorce, he believes they can if the person they are with loves them for what they are regardless of the circumstances. This inspires Juno to leave a note on Vanessa’s doorstep telling her she’s still interested in giving her her child for adoption, with or without Mark. She also tells Bleeker that she loves him. Bleeker reciprocates.
Mark leaves Vanessa for a loft in the city, and Juno has a baby boy while Bleeker is winning his track meet. When she isn’t in the stands he figures out that she’s in labor and runs to the hospital. As they lay together, both having decided not to see the child, she weeps at her loss. Vanessa is at the hospital and we see her dream fulfilled as she embraces her baby boy for the first time. As Summer comes we see that Juno is happy. With her guitar on her back she hops on her bicycle and goes to Bleeker’s house, where he’s waiting with his guitar, ready to play music with his girlfriend on a beautiful summer day.