Act I
In County Durham, the 1984–85 coal miners' strike is just beginning ("The Stars Look Down"). Motherless eleven-year-old Billy stays behind after his boxing class to give keys to Mrs. Wilkinson, who runs a ballet class. The class is all girls, but Billy is attracted to the grace of the dance ("Shine"). At first, Billy's interest in dance is easily concealed from his family, as the only person home at the time is his grandmother. She reveals to Billy the abuse she suffered at the hands of her late husband, but that she found great joy in dance ("Grandma's Song").

While his father Jackie, brother Tony and neighbours are on strike and clash with riot police, Billy secretly takes dance lessons ("Solidarity"). During the number, the violent reality of the strike is contrasted with the peaceful practise of ballet.

Eventually, Jackie discovers Billy in the ballet class and forbids him from attending the lessons. Mrs. Wilkinson, who recognizes Billy's potential, privately suggests that he should audition for the Royal Ballet School in London, offering free private lessons to prepare him for the audition. Billy is not sure what he wants to do, so he visits his best friend Michael for advice. He finds Michael wearing a dress. Michael persuades Billy to have fun with him by dressing up in woman's clothing, rejecting the restrictive inhibitions of their working class community ("Expressing Yourself").

For his first private ballet lesson, Billy brings things to inspire a special dance for the audition, including a letter from his mother ("Dear Billy (Mum's Letter)"). Through his lessons, he develops an impressive routine for his audition ("Born to Boogie"), as he forms a close bond with Mrs. Wilkinson. Her daughter, Debbie, tries to discourage Billy from auditioning because she has a crush on him. Meanwhile, Jackie and Tony are engaged in daily battles with riot police that often turn bloody. They struggle to support the family with very little in strike and union pay, a difficult task as the strike goes on for nearly a year.

When the day of the Royal Ballet School audition comes, the police come through the village, injuring Tony. Billy's family and some members of the community are gathered at the Elliot home, where Mrs. Wilkinson arrives when Billy fails to meet her to leave for the audition. She reveals that she has been teaching Billy in preparation for this audition, which upsets and angers Jackie and Tony. Tony tries to force Billy to dance on the table in front of everyone. Suddenly, the police approach and, as everyone escapes, Billy calls out to his father saying that his mother would have let him dance, to which Jackie says, "Your Mam's dead!". Billy goes into a rage ("Angry Dance"), and from that moment on, he stays away from anything related to ballet.

Act II
Six months later at the miner's annual Christmas show, the children put on a show disparaging Prime Minister Margaret Thatcher, who is seen as the antagonist by the coal miners ("Merry Christmas, Maggie Thatcher"). Billy's father gets drunk and sings an old folk song that elicits memories of his deceased wife and the usually stoic man leaves in tears ("Deep Into the Ground"). Left alone with Billy in the Community Centre, Michael reveals he has feelings for him, but Billy says that the fact that he likes ballet does not mean that he is gay. Michael gives him a kiss on the cheek. Michael tries to get Billy to show him some dancing, but Billy is sad and tells him to leave.

Michael departs, but leaves a music player running. Billy feels like dancing for the first time since the day of the aborted audition and dances while dreaming of being a grown-up dancer ("Swan Lake"). Unknown to Billy, his father arrives and watches him dance. Overcome with emotion, Jackie goes to Mrs. Wilkinson's house to discuss Billy's prospects as a dancer. She confirms Billy's talent, but is not sure whether or not he would get into the Royal Ballet School after missing the audition. Mrs. Wilkinson offers to help pay for the trip to London for the next audition, but Jackie refuses and leaves, questioning his working-class pride and the future mining has for his boys.

Jackie decides the only way to help Billy is to return to work. When Tony sees his father cross the picket line, he becomes infuriated and the two argue over what is more important: unity of the miners or helping Billy achieve his dream ("He Could Be A Star"). The argument comes to blows and Billy is hit accidentally. A miner chastises them for fighting and says that the important thing is looking after the child. One by one, the miners give money to help pay for the trip to the audition, but Billy still does not have enough for the bus fare to London. A strike-breaker arrives and offers him hundreds of pounds. An enraged Tony attempts to shun his donation, but no one else speaks up in his support. Now drained of hope, Tony dismally ponders whether there's a point for anything anymore, and runs off.

Billy and his father arrive at the Royal Ballet School for the audition. While Jackie waits outside, an upper-crust Londoner highlights the contrast between the Elliots and the families of the other applicants. Jackie meets a dancer with a thick Northern accent, who confesses that his father does not support his ballet career, but sharply advises Jackie to "get behind" his boy. Billy nervously finishes the audition with a feeling that he did not do well. As he packs his gear, he becomes overwhelmed and punches another dancer. The audition committee reminds Billy of the strict standards of the school and their zero-tolerance on violence. They have received an enthusiastic letter from Mrs. Wilkinson explaining Billy's background, situation and talent/potential; then ask him to describe what it feels like when he dances. Billy responds with a heartfelt declaration of his passion ("Electricity").

Back in Durham, the Elliots resume life, but times are tough and the miners are running a soup kitchen to ensure everyone is fed. Eventually, Billy receives a letter from the school and, overwhelmed and fearful, knowing that it heralds the end of the life he has known, informs his family that he was not accepted. Tony retrieves the letter from the waste bin and discovers that Billy had lied and actually was accepted - the family rejoice. At the same time, the miners' union has caved in; they lost the strike. Tony laments that miners are "dinosaurs", that by the time Billy returns home, all surrounding village's men will be jobless. Billy visits Mrs. Wilkinson at the dance class to thank her for everything she did to help him. Debbie is sad that Billy will be leaving.

Billy packs his things for the trip to the school and says goodbye to the soon-to-be-unemployed miners who are returning unhappily to work ("Once We Were Kings"). Billy says goodbye to his dead mother, who often visits him in his imagination ("Dear Billy (Billy's Reply)"). Billy breaks the fourth wall and begins to walk down the center aisle before Michael stops him to say goodbye. Billy drops his suitcase and runs onto the stage to give Michael a kiss on the cheek. Billy then walks back off stage, retrieves his suitcase and walks out toward his future alone.

The entire cast comes out on stage and calls Billy back to celebrate the bright future ahead of him ("Finale").