Act I
The musical begins with a performance by the band No Vacancy. The band's guitarist, Dewey Finn, repeatedly attempts to upstage the lead singer ("I'm Too Hot for You”) which leads to the band agreeing to kick him out for his antics after Dewey leaves the stage. The next morning, Dewey is awoken in his bedroom by his longtime friend, Ned Schneebly, and Ned's domineering girlfriend, Patty Di Marco. Patty demands rent from Dewey while Ned cowers behind her. After they leave, Dewey goes about his day, getting kicked out of his band and fired from his job at a record store, all while dreaming about getting his break and becoming a superstar ("When I Climb to the Top of Mount Rock"). Afterwards, Dewey receives a call from Rosalie Mullins, principal of the prestigious Horace Green School. She asks to speak to Ned, saying that the school has an open substitute teacher position that will pay over nine hundred dollars a week—enough to meet the rent. Pretending to be Ned, Dewey accepts the position.

At Horace Green, Rosalie does her best to keep everything running smoothly while greeting parents who come to drop off their children ("Horace Green Alma Mater"). Dewey arrives late both hungover and unprepared for the day, and the principal warns that "Ned" will be expected to meet the school's high standards ("Here at Horace Green"). Dewey enters his classroom and introduces himself as Mr. Schneebly. His thirteen students are immediately wary of him, and one of them, uptight Summer Hathaway, attempts to explain to him how the classes manage, and Dewey is disgusted by the rigid system. With no food to treat his hangover, Dewey spends most of the day sleeping, leaving the students to run wild.

At the apartment, Patty asks Ned to go on a jog with her, but he declines, claiming he has a lot of papers to grade. Understanding, Patty goes. However, as soon as she's gone, Ned pulls out his Guitar Hero console and begins playing. When Dewey comes home, he joins Ned and they discuss various topics such as teaching and their old band ("Variation 7”). After their game, Dewey attempts to convince Ned to rejoin him in their music career, by reminding him of all the perks of being a rockstar ("Children of Rock”). However, Patty arrives and breaks up the men's reminiscing session. Angry at Dewey, Patty reminds him that he's nothing more than a dreamer who will never succeed in the rock business, and gives him an ultimatum: pay the rent in thirty days, or they will kick him out ("Give Up Your Dreams”).

The next day at school, Dewey argues with another teacher and hears music coming from one of the classrooms. Upon learning that his students are in music class with Rosalie ("Queen of the Night"), he inquires in amazement about what instruments they play. Dewey then tells his students that they're now a part of his new band set to compete in the Battle of the Bands. First, he puts together the instrumentals of his band: Zack on electric guitar, Katie on bass guitar, Lawrence on keyboards, and Freddy on drums. He also makes two of the girls—Shonelle and Marcy—backup singers, and two other girls—Madison and Sophie—roadies. Then he moves onto technical jobs. Mason is put in charge of lights, James is made the security officer, and an ecstatic Billy is made the band's stylist. Summer is angry that she hasn't been given a job and says "groupies are sluts" in response to Dewey's first suggestion. Dewey then makes her the band's manager. The only student left without a job is Tomika, the shy new girl ("You're in the Band"). Confident about their prospects, Dewey hands out famous CDs to the students to listen to as homework ("You're in the Band (Reprise)”).

The children go home, and a glimpse is seen in some of their home lives. Freddy tells his father about the music he was assigned to listen to, but his father belittles him, saying that he's not smart like the other children at Horace Green. In another part of town, Billy is reading a Vogue magazine disguised as Sports Illustrated on account of pressure from his father to take up football. Elsewhere, Tomika tells her fathers that she's not making friends or doing well in her new school, but her parents dismiss her since they love Horace Green. Finally, Zack attempts to talk to his father about his day, but his father is on a business call and shouts at Zack for trying to speak to him, telling him to go away. Frustrated, Zack, Tomika, Billy, Freddy, and the other students lament that they have so much to tell and offer their parents and the world, but they just won't listen to them yet ("If Only You Would Listen"). Later, Shonelle and Marcy say that they should call the band School of Rock. Dewey loves it, and makes up a song to create the impression that he is prepared ("In the End of Time (A Cappella Version)").

In the Faculty Lounge, the other teachers complain that the children have become undisciplined under Dewey ("Faculty Quadrille"). In the classroom, the band continues practicing Dewey's new song ("In the End of Time (Practice Version)"). After playing, Dewey tells everyone they're doing great. However, Zack is playing in an uptight and rigid manner, and Dewey says that Zack needs to get angry at "the Man" in order to really rock. He explains that the man is responsible for everything wrong with the world, and Dewey and the kids get angry and shout about how they're going to stick it to the Man ("Stick it to the Man"). On account of being stuck in school, Dewey and the kids end up sneaking out of the building in order to make it to the Battle of the Bands auditions on time. The children and Dewey sadly arrive late at the auditions. With the manager about to leave, Summer convinces him to stay with a lie about a terminal illness and the class is able to compete ("In the End of Time (The Audition)"). They qualify and celebrate their success ("Stick it to the Man (Reprise)").

Act II
Thirty-six hours before the Battle of the Bands, the students are hard at work preparing for the event while Dewey attends a faculty conference. The students conclude that the one outstanding issue is the costumes, which Billy has yet to show anybody. He argues that they aren't finished yet, but Summer makes him show them anyway. Using Lawrence as an unwilling model, Billy shows everyone, and they hate them. Annoyed but not disheartened, Billy goes back to the drawing board ("Time to Play"). At the faculty meeting which Rosalie uses to stress the importance of parents' night, Dewey discovers that she is secretly a rocker, and loves Stevie Nicks. Dewey panics when he gets back to the classroom and begins to think of a cover. Tomika summons the courage to speak to him saying that she wants to sing. When Dewey asks why she didn't respond to the call for backup singers, she states that she's a lead singer and can’t sing backup . Although initially too nervous, Tomika begins to sing when others are not looking and it turns out that she has the voice of a perfect angel ("Amazing Grace").

Upon hearing that Rosalie is coming, students quickly cover their instruments with Thanksgiving-themed items and Dewey breaks into a fake lesson. When she challenges this, Dewey accuses other teachers of being on crack before admitting that he uses music to teach "boring" subjects. After arguing that there are no boring subjects, Rosalie announces that she will be sitting in for the rest of Dewey's lesson. Nervous, Dewey pulls out his guitar and improvises a song about math ("Math Is a Wonderful Thing"). Rosalie is unimpressed, but Dewey decides to ask her out to a bar regardless. Later that night, Rosalie and Dewey meet at the bar, and, after having a few drinks, Dewey plays a Stevie Nicks song on the jukebox, causing Rosalie to let loose and laments about how she feels she has lost her inner music. Stating that Dewey has reminded her about it, she promises that if the parents' meeting goes well the next day, she will help Dewey and School of Rock go to the Battle of the Bands ("Where Did the Rock Go?"). Dewey impulsively kisses Rosalie, and they part ways.

Dewey arrives home just as Patty and Ned are going through the mail. Prompted by the discovery of Dewey's paycheck made out to Ned, Dewey explains his impersonation idea. Ned goes into a panic attack, but Dewey manages to calm him down and make him promise not to tell Patty. The next day, the students go to rehearse their song, but then Zack reveals that he wrote his own song for the band in his free time. Dewey is floored by Zack's talent, and has Zack teach the song to the rest of the band ("School of Rock (Band Practice)"). However, in the middle of the practice, Rosalie unwittingly brings the students' parents into the classroom, and they are appalled by what is going on. Focusing on the talent of each child, Dewey slowly convinces the parents to see the band in a positive light until Patty and Ned burst in. Having extracted the information from Ned, Patty reveals that Dewey is not Ned Schneebly and sends the parents into a rage, and Dewey and the children escape in the commotion ("Dewey's Confession").

As Rosalie paces nervously in the halls, she finds Mason and reminds him that Dewey isn't who the students think he is. Mason counters that he is a role-model regardless of his name. Touched by this, Rosalie misleads the parents to buy the children more time. The children use this time to reinvigorate Dewey who has given up on his dream and returned to his room. Led by Tomika, they all explain how much they need him ("If Only You Would Listen (Reprise)"). Discovering that they stole the bus to head to the Battle, Dewey's dream is reignited ("Stick it to the Man (Reprise)"). Patty makes one last attempt to stop them, but Ned finally stands up to her and accompanies them to the Battle. The band arrives just as No Vacancy is finishing up their performance ("I'm Too Hot for You (Reprise)"). Dewey decides that they should play Zack's song and accepts new costumes from Billy. The parents arrive but are not allowed backstage by the security guards. As the students go to perform, Zack's father begins shouting at his son not to go onstage, telling him that School of Rock is ridiculous and stupid. Finally having enough, Zack stands up to his father and tells him that the band means more to him than he does, and then goes to play with the band.

The School of Rock performs Zack's song, and the crowd goes wild. Their parents watch on from an empty box seat, and each of them slowly fall in love with the band and how amazing their children are. Each of the instrumental students gets a solo, and Tomika sings lead with Dewey as well. By the end, Zack's father is frozen with pride and has to be pulled away by Summer's mother ("School of Rock (Teacher's Pet)"). After the performance, Rosalie and the band's parents congratulate the group, as well as Ned who has decked out in full heavy metal gear for the Battle. Dewey watches the parents and their kids, and finally feels as though he has accomplished something worthwhile. Patty then enters with a police officer and tries to get Dewey arrested for fraud, but Rosalie convinces the officer that Mr. Finn is Horace Green's official Band Coach. The winner of the competition is announced as No Vacancy, but Dewey assures everyone that winning didn't really matter because they did something even more special. To please an enthralled crowd, the band plays an encore ("Stick It to the Man (Encore)"). After their song, Dewey and Rosalie kiss again, and Rosalie mixes her classical singing with the heavy rock music of School of Rock, implying that a change is coming to Horace Green and its curriculum because of the band and Dewey ("Finale").