Junie B.'s Essential Guide to School JR. begins with a brilliant idea by Junie B. Jones: with one-and-a-half years of school under her belt, she's going to create a guide for surviving school! Her classmates are enthusiastic about the idea ("Junie B.'s Essential Survival Guide To School"). At class that day, Junie B.'s classmates try to get her to discuss her ideas for the book, but Junie B. secretly doesn't have any ideas ("Like What?"). During this exchange, Junie B. gets a little too excited and calls students bad names in class. Her teacher, mr. Scary, sends her home with a note ("Shoo Bee Doo Bee"). Junie B. gives the note to her Mother.

The next day at school, Junie B.'s classmate Sheldon approaches her with an idea for the book: backpacks ("Backpacks On Parade"). Many of the students support the idea, complimenting Sheldon, but Junie B. is jealous and worried that he is getting credit for her idea ("A Great Idea - Parts 1 and 2"). Junie B. throws a tantrum and is sent home with another note. When she is discussing her tantrum with her mother that evening, she explains that her anger comes from a bull that lives inside her stomach ("El Toro Fabuloso").

During lunch the next day, the school's fashionista, Lucille, interviews Junie B. about school clothes ("Some Stuff About Clothes"). Junie B. tells her that her favorite clothes include giant pockets, telling a story about a potato she once found that fit perfectly in her pocket (Potato On The Sidewalk!). However, during Junie B.'s interview, her classmate May steals the attention. Junie B. responds by intentionally spilling spaghetti on May ("El Toro Fabuloso - Reprise"). At home that evening, Junie B.'s family encourages her to make up with May.

The next day, the students perform a play at school all about school supplies ("School Supplies - Parts 1 and 2"). The play, written and organized by May, gets derailed when Junie B. angrily goes offscript and charges at May ("El Toro Shoo Bees"). With her mother's encouragement, Junie B. writes an apology letter to May that night. In the morning, Junie B. chases after the bus with all of her classmates onboard ("Gotta Get There"). After Junie B. boards the bus, Herb wants to discuss his chapter of the book with her: the rules of the school bus ("Bus Rules"). However, Junie B. takes over, insisting that one of the best things to do on the bus is to make funny faces. She does this out the window, prompting a horrified passing driver to take a picture with her cell phone.

After the driver emails the rude pictures of Junie B. to the Principal, Junie B. is forced to face the consequences of her actions ("Principal's Office"). The principal, along with a few of Junie B.'s school role models, urge Junie B. to respect the school's rules. While the adults are discussing this with Junie B., they form a plan. The principal tells Junie B. to spread the word that there are no rules for her classroom the rest of the day. Junie B. happily tells her classmates, but the students soon realize that without rules, many of the good parts of the day are ruined. They all agree that rules are important and should be followed ("Rules - Parts 1, 2, and 3").

In the schoolyard later that day, students are enthusiastically toting around their report cards ("Report Card Day"). Junie B., however, resorts to burying her report card in a neighbor's yard. Her mother quickly stops her and shows Junie B. her own report from many years ago. As it turns out, her mother wasn't a perfect student either ("Mother Was A Bad Kid Too"). This comforts Junie B., who returns her attention to her survival guide. Just as she wonders who will help her with this daunting task, May appears at her door. The two girls make up. ("The Things You Learn Along The Way"). The students complete their survival guide ("Junie B.'s Essential Survival Guide Bows").