Junie B. Jones, The Musical, opens on an empty stage with a huge "top secret personal beeswax journal" that opens and serves as the backdrop. Junie B. Jones pops out from behind it and begins skipping, with a journal in her hand. She explains that her mother bought her this journal at the store and told her that she can fill it with anything she wants. As the rest of the cast enters, she tells them how she got her name: "Junie" for the month of June and "B." for Beatrice. Then she introduces her family: Mother, Daddy, Baby Ollie and her pet dog, Tickle. Junie B. goes to Clarence Somebody or other elementary school and is getting ready for first grade. She plans to fill her journal with all of her upcoming adventures ("Top Secret Personal Beeswax").

When Junie B. arrives for her first day of first grade, she realizes that it's going to be a bit different from kindergarten. Her kindergarten best friend, Lucille, has ditched her for two new best friends, Camille and Chenille, in part, because their names all rhyme ("Lucille, Camille and Chenille"). Junie B. laments that nothing rhymes with Junie.

On the school bus, Junie B. finds that her other best friend, Grace, has found a new seatmate, Bobbi Jean Piper. Junie B. makes a fuss and gets yelled at by the bus driver, Mr. Woo. Junie B. ends up sitting next to Herb, a boy who is new to the school and doesn't have any friends. Herb offers to be her friend – just for today – but Junie B. soon realizes that she and Herb have a lot in common and she wants to be long term friends ("You Can Be My Friend").

Back at school, Junie B. is getting to know the kids in her class. There's bossy-headed May, Jose (who speaks Spanish and English) and Lennie. Their teacher, Mr. Scary (Junie B. thinks he made that name up) instructs them to choose a word from the list on the chalkboard and draw a picture of it. As Junie B.'s classmates happily work on their drawings, she realizes something is wrong: she can't make heads or tails of the words on the chalkboard. This can only mean one thing, Junie B. Jones needs glasses! ("Time to Make a Drawing").

With her new purple glasses, Junie B. worries that the kids at school will make fun of her. Her mother tries to tell her that true friends don't worry about what you look like. In Mr. Scary's class, Junie B. brings her glasses out for show and tell ("Show and Tell"). When May begins to make fun of her, Herb says that Junie's glasses look really cool, and everyone agrees ("Now I See").

Junie B.'s next adventure starts when she finds a surprise that her mother has left for her in the kitchen: a brand new lunch box. Junie B. excitedly takes it to school and shows it off ("Lunch Box"). However, she quickly learns that she and Sheldon are the only two people who brought lunch today; everyone else is buying hoagies. Herb gets a cookie with his lunch, and Junie B. is jealous, so Herb shares with her. The cookie tastes just like the kind they used to get in kindergarten, made by the legendary lunch lady, Mrs. Gutzman, the Queen of Snacks. The kids tell Herb all about her ("Gladys Gutzman").

Mrs. Gutzman appears and explains that, while kindergartners get cookies, the first graders have to buy them with their lunches. Junie B. wants to know what the children who bring their lunches are supposed to do about cookies, and Mrs. Gutzman has an idea: she gives Junie B. a chance to help her out working in the kitchen. Junie B. is excited at the idea of becoming the "Boss of Lunch," but it soon becomes clear that she doesn't know much about working in the kitchen. When Mrs. Gutzman asks Junie B. to introduce the lunch to the other kids, Junie B. announces to everyone that the lunch smells "stinkle." The kids get upset and rush out of the cafeteria without lunch. Everyone is very unhappy.

Mrs. Gutzman comes looking for Junie B. in the classroom. Junie B. tries to hide, but May points her out to Mrs. Gutzman. Mrs. Gutzman explains that she has something for the class, but she needs an experienced helper to pass it out. Junie B. is concerned because the children are still mad at her from the lunchroom incident. Mrs. Gutzman solves that: she has brought sugar cookies for the class, and she tells everyone that Junie B. Jones gave her the idea. Junie B. joyfully hands out the cookies, having learned a lesson that, even if you goof up sometimes, you can make things better with kind words, good friends and sugar cookies ("Beeswax Cookie Reprise").

Next, Junie B. and her classmates prepare for the kickball tournament ("Kickball Tournament"). While practicing, Junie B. kicks a full watering can and hurts her toe; she won't be able to play in the tournament. Mr. Scary tries to think of another way that Junie B. can play in the tournament. Sheldon, who also can't play in the tournament, is going to perform the halftime show and invites Junie B. to join him ("Sheldon Pott's Halftime Show")

After school, Mother and Daddy learn that Junie B. is not excited about the halftime show. She wanted to play in the kickball tournament to be the star and get all of the attention. Mother points out that no one can be the star all the time, but this does not satisfy Junie B. Daddy knows that Junie B. is disappointed, but he and Mother encourage her to try and take her sour situation and make it sweet ("When Life Gives You Lemons"). It turns out that Daddy knows how to juggle, and he will teach Junie B. how to do it so that she can perform at the halftime show

A week later, when the big day arrives, despite lots of hard work and practice, Junie B. still can't juggle. The kickball tournament begins ("Kickball Tournament – Reprise"). Suddenly, it's halftime and Sheldon is too nervous to perform. He runs offstage, and Junie B. is left alone in front of the crowd, with nothing to do but play the wooden block. The spectators are not impressed and begin throwing food at her. As Junie B. tells them off, she realizes that she has three biscuits in front of her and she begins to juggle them. Everyone is impressed, especially Mother and Daddy, who are proud of Junie B. because she practiced and practiced and never gave up, which makes her a star! ("When Life Gives You Lemons – Reprise").

Junie B. comes to the last page of her journal and gets upset. There's no more room, so that means she can't have any more adventures. Herb rips out some pages from his notebook and gives them to her, so they can keep having more adventures together. Before joining Herb on the bus, Junie B. tells the audience what she has learned from her adventures: growing up is scary, but it's also really fun, so she's writing down the story of her life. As Junie B. gets on the bus with Herb, everyone joins in, telling her to keep writing ("Writing Down the Story of My Life").