After her client Albert Osborne (Robert Benchley) makes a pass at her, Susan Applegate (Ginger Rogers) quits her job as a scalp massager for the Revigorous System and decides to leave New York City and return home to Stevenson, Iowa.

Upon arriving at the train station, she discovers she has only enough money to cover a child's fare, so she disguises herself as a twelve-year-old girl named Su-Su. When a suspicious conductor catches her smoking, Su-Su takes refuge in the compartment of Major Philip Kirby (Ray Milland) who, believing she is a frightened child, and agrees to let her stay with him until they reach his stop.

When the train is detained by flooding on the tracks, Philip's fiancée Pamela Hill (Rita Johnson) and her father, his ommanding officer at the military academy where he teaches, drive to meet him. Pamela boards the train and finds Su-Su sleeping in the lower berth in his compartment. Imagining the worst, she accuses Philip of being unfaithful and reports his alleged infidelity to her father. Indignant, and still feeling protective of Su-Su, Philip insists on bringing her to the school where her parents can retrieve her, and the Hills agree to let her stay with them.

Pamela's teenaged sister Lucy (Diana Lynn) immediately sees through Susan's disguise. She promises to keep her secret if Susan will help her sabotage Pamela's efforts to keep Philip at the academy instead of allowing him to fulfill his wish to be assigned to active duty. Pretending to be Pamela, Susan calls one of the woman's Washington D.C. connections and arranges to have Philip's status changed.

Susan becomes popular with the young students, especially cadet Clifford Osborne (Frankie Thomas), unaware he is the son of the client who prompted her to quit her job. When the elder Osborne visits the school, he recognizes Susan and reveals her identity to Pamela, who threatens to expose her and Philip and create a public scandal unless Susan leaves immediately.

Susan returns home, but continues to fantasize about Philip, much to the dismay of her fiancé Will Duffy (Richard Fiske). When Philip stops to visit her on his way to California to report for active duty, she pretends to be her own mother and Philip leaves without learning the truth. After Philip leaves, Pamela discovers that Philip has married someone else, and she rushes to the train station to confess her deception, and she and Philip decide to marry in Neveda while en route to his army base.

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The screenplay was written by Billy Wilder and Charles Brackett and was based on the play Connie Goes Home by Edward Childs Carpenter. Billy Wilder had arrived in Hollywood in 1934 and during the ensuing years, he and Brackett had collaborated on eight screenplays, including “Ninotchka” and “Ball of Fire”, but Wilder was anxious to try his hand at directing and producer Arthur Hornblow, Jr. agreed to give him a chance. Wilder was determined to make a mainstream film that would be a box office success so he wouldn't be relegated to a typewriter for the rest of his career.

Paramount Pictures owned the screen rights to the play Connie Goes Home, which Wilder thought was the perfect vehicle for Ginger Rogers, and he and Brackett wrote the role of Philip Kirby with Cary Grant in mind.

Rogers recently had won the Academy Award for Best Actress for “Kitty Foyle” and now was in a position to select her own director. Agent Leland Hayward represented both Rogers and Wilder, who asked him to intercede with her on his behalf, and Brackett also urged her to meet the novice director. She agreed, and she and the screenwriters met during the filming of ”Roxie Hart”. They pitched the film during lunch at an Italian restaurant, and Rogers later recalled:

“Mr. Wilder was charming, a European gentleman . . . I've always been a good judge of character. I decided then and there that we would get along and that he had the qualities to become a good director . . . I felt he would be strong, and that he would listen. He certainly understood how to pay attention to a woman."

What also appealed to Rogers was the basic concept of the film. As a younger woman, she had pretended to be eligible for a child's fare when traveling by train with her cash-strapped mother on more than one occasion, so she easily identified with the plot and agreed to make the film. In fact, Ginger asked Wilder if her own mother, Lela Rogers, could be in the movie with her. Wilder agreed and cast her as Susan’s mother at the end of the movie.

Wilder was driving home from the studio one evening and pulled up at a red light next to Ray Milland. Impulsively, he called out, "I'm doing a picture. Would you like to be in it?" and the actor responded, "Sure." Wilder sent him the script, which Milland liked. Three years later the two men would collaborate on “The Lost Weekend”, which would win Oscars for both of them.

In Nobody's Perfect, Charlotte Chandler's biography of Wilder, the director shared some insights on “The Major and the Minor”:

"Everybody was sure I was going to do some German Expressionist thing sure to fail, and that crazy Wilder would go back to his typewriter and stop bothering everybody. But I was very careful. I set out to make a commercial picture I wouldn't be ashamed of, so my first picture as a director wouldn't be my last...I wrote the part of the major for Cary Grant. I always wanted him in one of my pictures, but it never worked out...It wasn't too difficult for Ginger to imitate a girl of twelve, especially in those days. Now it seems a little foolish. To think a thirty-year-old could play a twelve-year-old girl and be believable! Well, she couldn't, but it didn't matter. The audiences were very generous in those days. They had come to have a good time and they went along with you."

“The Major and the Minor” was a critical and box-office hit, launching Wilder's long and successful directing career. The film was remade as “You’re Never Too Young” in 1955. The gender-reversal version starred Jerry Lewis as the adult disguised as a child and Diana Lynn as the woman who helps him. Diana was also the actress who portrayed teenager Lucy Hill in the original.