While largely based on the original series, with storylines from three of the picture books weaved into the plot, several liberties were taken with the characters' backstories, most notably Madeline who is depicted as an orphan in the film; the 1939 book explicitly states the dollhouse as coming from her Papa, and she is seen with her parents and two siblings in Madeline's Christmas.

The film's costume department went for some artistic licence in developing the costumes for Madeline. Aside from moving the time period to 1950s Paris, the producers elected for saturated blues and reds in the students' uniforms while keeping them as believable as possible; greys were immediately ruled out as "being depressing". Similar considerations were made for Frances McDormand's character, a novice nun who, according to research, would have worn a short black habit; a softer blue habit similar to the one worn by Miss Clavel in the books was used instead.

In 1956 Paris, France, a young girl named Madeline attends a boarding school run by Miss Clavel, a no-nonsense, strict, but caring nun. She is the only orphan and wishes she had a family since her parents died when she was very small. She goes on daily walks, eats her favorite meal, "Chicken Hélène" (a chicken dish named after the cook, Hélène, who makes it), and often causes mischief for Miss Clavel. One night, Miss Clavel feels that something is not right, so she runs up to the girls' room and finds Madeline groaning in pain on her bed. Quickly, Hélène dials the hospital, who explains to Miss Clavel that they must take out Madeline's appendix immediately. During her stay in the hospital overnight, after the surgery, Madeline wanders down the hallway, and finds Lady Covington. The two begin to talk, and Lady Covington reveals to Madeline that she carved her name under Madeline's bed, Marie Gilbert. She asks Madeline to see if it's still there. Their conversation is interrupted by the strict Lord Covington, who orders Madeline to leave. A few days later, when Madeline is ready to go, she and Miss Clavel discover that Lady Covington had died. She then sees a chicken in Hélène's car, and finds out that Chicken Hélène that will be served that night.

Filmed in Paris in 1997, the story is set in 1956, rather than 1939. Many of the landmarks from the books appear in the film, although some were too crowded with modern traffic to be used. A relative newcomer, Hatty Jones was picked among thousands of applicants in a casting search, which was looking for the girl with "the right height and charm for the role".

Madeline was released on VHS (which is part of the Columbia TriStar Family Collection series) and DVD on December 15, 1998.