Act 1
Charlie Price grows up as the fourth-generation "son" in his family business, Price & Son, a shoe manufacturing company with its factory in Northampton. Another young boy, growing up in London, is as fascinated by shoes as Charlie is bored by them. But in this case, it is a pair of red women's heels that have attracted his attention, aggravating his strict father. Years pass. Charlie's father is aging and hopes Charlie will take over the factory. Still, Charlie is eager to move to London with his status-conscious fiancée, Nicola, and pursue a real estate career ("The Most Beautiful Thing").

Charlie has barely made it into his new flat in London when his father dies suddenly. Charlie hurries home for the funeral, where he finds the factory near bankruptcy. The factory makes good quality men's shoes, but they are not stylish and not cheap, and the market for them is drying up. Charlie is determined to save the factory and his father's legacy, though he has no desire to run Price & Sons himself. The workers, many of whom have known Charlie his entire life, do not understand why Charlie moved away in the first place, and many are hostile and skeptical of the new management.

Returning to London, Charlie meets his friend and fellow shoe salesman, Harry, in a pub to ask for help. Harry can only offer a temporary solution and advises Charlie not to fight the inevitable ("Take What You Got"). Leaving the pub, Charlie witnesses a woman being accosted by two drunks. He intervenes and is knocked unconscious. He comes to in a seedy nightclub, where the woman he attempted to rescue is revealed to have been the club's drag queen headliner, Lola, who performs with her backup troupe of drag dancers, the "angels" ("Land of Lola"). Recuperating from his ordeal in Lola's dressing room, an uncomfortable Charlie notices the performers' high-heeled boots are not designed to hold a man's weight. Lola explains that the expensive and unreliable footwear is an essential part of any drag act.

Charlie returns to the factory and begins reluctantly laying off his workers. Lauren, one of the women on the assembly line, explodes at Charlie when given her notice and stubbornly tells him that other struggling shoe factories have survived by entering an "underserved niche market." This gives Charlie an idea ("Land of Lola" {Reprise}), and he invites Lola to come to the factory to help him design a women's boot that can be comfortable for a man ("Charlie's Soliloquy"/"Step One").

Lola and the angels arrive at the factory, and she is immediately dissatisfied with Charlie's first design of the boot. Quickly getting the women of the factory on her side, she draws a quick design of a boot, explaining the most important factor is by far the heel ("The Sex is in the Heel"). George, the factory manager, realizes a way to make her design practical. An impressed Charlie begs Lola to stay until a prestigious footwear show in Milan in three weeks to design a new line of "kinky boots" that could save the factory. Lola is reluctant since she is already receiving crass comments from Don, the factory foreman, and some of the other factory workers but is flattered by Charlie's praise and finally agrees.

Charlie announces that the factory will be moving ahead with production on the boots. He thanks Lauren for giving him the idea and offers her a promotion. She accepts and is horrified but thrilled to realize she is falling for him ("The History of Wrong Guys").

The next day, Lola shows up in men's clothes and is mocked by Don and his friends. An upset Lola takes refuge in the bathroom, and Charlie attempts to comfort her. Lola explains that her father trained her as a boxer but disowned her when she showed up for a match in drag. The two discover their similarly complex feelings toward their fathers, and Lola introduces herself by her birth name: Simon ("Not My Father's Son").

Nicola and her boss Richard Bailey arrive from London and present Charlie with a plan for the factory that Richard has drawn up: closing it and converting it into condominiums. Charlie refuses but is shocked to discover that his father had agreed to this plan before he died, presumably because Charlie was not there to run it. He refuses to sell, and soon the workers are celebrating as the first pair of "kinky boots" is finished ("Everybody Say Yeah").

Act 2
Some of the factory workers are not enthusiastic about the radical change in their product line. Some of them, especially the intimidating Don, make Lola feel very unwelcome. Lola taunts him back, enlisting the female factory workers' help to prove that Lola is closer to a woman's ideal man than Don ("What a Woman Wants"). Lola presents Don with a unique wager to see who is the better "man": Lola will do anything that Don specifies if Don will do the same thing for her. Don's challenge is for Lola to fight him in a boxing match at the pub. Charlie, remembering Lola's background, is horrified. Lola easily scores against Don in the ring but ultimately lets Don win the match ("In This Corner"). Afterward, Don asks why she let him win, and Lola replies that she could not be so cruel as to humiliate Don in front of his mates. She gives him her part of the challenge: "accept someone for who they are."

Charlie is pouring his own money into the factory to ensure it will be ready in time for Milan, and he is getting frantic that the product is not right, angrily forcing his staff to redo what he considers to be shoddy work. Nicola arrives, fed up with Charlie's obsession over the factory, and breaks up with him. Lola has been making some decisions about production and preparations without consulting Charlie. When he discovers that she has decided to have her angels wear the boots on the runway rather than hiring professional models, an overwhelmed Charlie lashes out at her, humiliating her in front of the other workers. Lola storms out, and the factory workers go home. Alone, Charlie struggles with the weight of his father's legacy and what it means to be his own man ("Soul of a Man").

Lauren finds Charlie and tells him to come back to the factory. It is revealed Don has persuaded the workers to return to work and to sacrifice a week's pay to ensure the boots can be finished in time for Milan. Charlie is astonished and grateful and asks if Don has paid up on his wager by accepting Lola. Lauren explains that the person that Don has accepted is Charlie himself.

As he heads to the airport for Milan, Charlie leaves a heartfelt apology on Lola's voicemail. Meanwhile, Lola performs her act at a nursing home in her home town. After she leaves the stage, she speaks to her dying father, who uses a wheelchair, and reaches a sense of closure ("Hold Me in Your Heart").

Charlie and Lauren arrive in Milan. But without models, Charlie is forced to walk the runway himself. Lauren is thrilled by his dedication ("The History of Wrong Guys (Reprise)"), but the show threatens to be a disaster. Just as all seems lost, Lola and her angels arrive to save the day. Lauren and Charlie share their first kiss, and the whole company celebrates the success of the "Kinky Boots" ("Raise You Up/Just Be").