The film opens with Juno (Ellen Page) staring at a recliner while drinking from a gallon container of Sunny-D bug juice, telling us, "It all began with a chair", after which we see a flashback of Juno and her best friend, Paulie Bleeker (Michael Cera), who's sitting naked in a recliner, waiting for Juno, who removes her underwear and sits down on him [the extent of the sex scene to keep it PG-13].
Smart, fast-mouthed Juno then goes into a convenience store to take a pregnancy test. Judging by her conversation with Rollo the clerk (Rainn Wilson), this is her third test today (hence her drinking all the Sunny-D to produce urine). The third test shows the same result as the previous two: positive. Juno calls (on her hamburger phone) her best friend, Leah, who takes a few minutes to fully comprehend Juno's situation. We see a funny clip of Paulie getting ready to train with the track team, wearing his trademark head and wrist bands. As he exits the house, he sees Juno, who tells him the news.
Paulie supports Juno's decision to abort the baby; Juno goes to a women's clinic for an abortion, where she bumps into classmate and lone anti-abortion protester Su-Chin, who robotically tries to dissuade Juno from having an abortion. Out of all the arguments, the one that Juno finds remotely interesting is that her baby might have fingernails by now. She encounters a snarky receptionist who tries to give her boysenberry-flavored condoms. Juno eventually decides against the abortion. She meets up with Leah and the two discuss adoption and how to break the news to Juno's dad and step-mom, Mac and Bren (J.K. Simmons and Allison Janney).
Juno breaks the news to her folks, who while disappointed are supportive. Juno tells them she wants to give the baby to a couple she and Leah found in Penny-Saver. She also lets them know who the father is (Mac: "Next time I see the Bleeker kid, I'm going to punch him in the wiener"). Mac goes with Juno to visit the prospective parents, Vanessa and Mark Loring (Jennifer Garner and Jason Bateman). Vanessa can't have children and is very excited by Juno's offer. The couple's lawyer seems prepared to negotiate an open adoption wherein Juno is updated on the child's development after birth. However, Juno has no interest and would rather have a closed adoption. The couple seems taken aback by how nonchalant Juno comes off, despite her less-than-polite attitude.
While using their upstairs bathroom, Juno bumps into Mark, who is looking for something. Inspired by Mark's Les Paul guitar, the two discover compatible tastes in music and movies. Mark used to be in a rock band, though now he makes his living writing ad jingles. The two jam for a bit on the guitars, before Vanessa frustratingly interrupts so they can get back to business. The meeting concludes with Mark and Vanessa agreeing to pay for Juno's medical expenses.
Juno visits Paulie, and Paulie says that the two should get their band back together after Juno delivers. He also tries to suggest that the two should get back together as a couple, which Juno tries to play off, to Paulie's disappointment. She suggests he try to get together with Katrina De Voort, but Paulie doesn't like the idea, claiming Katrina and her house always smell like soup. Throughout, Paulie supports Juno's decisions and quietly tries to help her any way he can, while Juno doesn't pay much attention to Paulie's support, relying more on her parents, as well as the Lorings.
Juno goes with her mother and Leah for an ultrasound, at which the technician makes judgmental, condescending remarks about Juno's situation, whereupon Bren tells her where to put her comments, to Juno and Leah's amusement. Juno makes a few visits to the Lorings, mostly unexpected, where Mark is usually the only one home. The two begin hanging out, watching bad horror flicks and listening to music. We can see a chemistry forming between them. Eventually Vanessa comes home and Juno shows them pictures from the ultrasound. In a later scene, we see the Lorings in the baby's future room: While Vanessa tries to figure out what to put on the wall, we sense that Mark isn't enthusiastic about being a father, When Juno comes home, Bren warns her about going to see the Lorings so much, especially while Vanessa isn't there, since it isn't appropriate. Juno shrugs off the advice. Juno later spies Vanessa at the mall, where she sees how great she is with the children of friends. The two notice each other, and Juno lets Vanessa feel the fetus.
At school, where she has to deal with being The Pregnant 16 YO, Juno is given nasty looks. She and Leah eat lunch by the school's trophy case, while Leah goes on about a few topics: One is her crush on a teacher, an older-guy thing she has; the other is Paulie asking Katrina to prom. While Juno denies she has any feelings for Paulie, later that day she confronts him and they quarrel. Paulie holds most of the moral high ground, claiming that Juno is acting immature, and how heartbroken he was when Juno claimed they were never a couple.
Juno makes another visit to the Lorings, where she and Mark listen to All The Young Dudes, which Mark says he danced to at his prom. The two slow dance to it in the basement, where Mark tells Juno he's leaving Vanessa. Juno is shocked and tries to convince him not to. While Mark believed Juno would be happy about the news, he learns that above all, Juno wants the baby to be raised in a loving family. Juno is about to leave when Vanessa comes home, sees that Juno is crying, and stops her, wanting to know what is going on. Mark admits that he isn't ready to be a father. Vanessa tells him that he needs to grow up and accept that he isn't going to be a rock star. The two quarrel as Juno sees herself out. She goes home and talks to her father about her need to know that people can be happy with each other. Mac tells her that she'll know she's in love when she finds the person that loves her for her, no matter what situation she's in; she arrives at the realization that that person is Paulie.
As the Lorings discuss their pending divorce, Juno rings their doorbell and leaves them a note: "If you're still in, I'm still in". She then buys a ton of orange tic-tacs (Paulie's vice) with Leah, and leaves them in Paulie's mailbox, to his amusement. After school, Juno goes to Paulie's track practice and tells him she's in love with him. (He's the one that accepts her for her, always looking at her face -- not her belly -- when they talk). Juno calls him the coolest person she knows, and says that he doesn't even have to try (Paulie: "I try really hard, actually"). They kiss while Leah teases from afar that it might induce labor.
At home, Juno's water breaks, and the family rushes to the hospital. Juno desperately wants a shot for the pain, referring to it as a Spinal Tap, after which she gives birth to a healthy baby. While she didn't want to disturb Paulie at his track meet, after winning his event and realizing Juno wasn't there, Paulie figures it out and rushes to the hospital, where they decide not to see the child after the birth. Paulie lies next to Juno and holds her while Vanessa goes to the nursery to hold her new baby. Vanessa asks Bren how she looks, and Bren sweetly replies, "Like a new mom: scared shitless."
Afterwards, we see Juno's wrapup, in which she reiterates that it all began with a chair, and ended with a chair (Vanessa's rocking chair). We see the baby's room, where Vanessa has put Juno's note on the wall. Bren finally adopts a puppy, having refrained up to now because while she loves dogs, Juno is allergic. Juno rides her bike over to Paulie's, where she talks about falling in love, then having babies, and how it didn't end up in that order for her. The two play Anyone Else But You on the guitar, after which they kiss.