The project began in 1996 when Steven Spielberg approached horror author Stephen King about making a haunted house film, and they collaborated on a screenplay based on Robert Wise's 1963 adaptation of The Haunting of Hill House, but creative differences ultimately ended their partnership.

After leaving the Spielberg-King project, Stephen King retooled his own version of the material into the 2002 miniseries Rose Red, which blends elements of Wise's 1963 film and Shirley Jackson's original novel.

Spielberg commissioned first-time screenwriter David Self to write a new script for the film and produced it through his studio DreamWorks Pictures, remaining an uncredited executive producer while occasionally visiting the set during filming.

Jan de Bont took over directing duties on The Haunting in a swap with Spielberg, who instead directed Minority Report; de Bont wanted to distance the film from the 1963 version and focus more directly on Shirley Jackson's novel.

Cinematographer Caleb Deschanel was originally hired to shoot the film but left over creative differences just one week into filming, and was replaced by Karl Walter Lindenlaub.

While the exteriors were filmed at Harlaxton Manor in England (with its Great Hall used for key interior scenes) and the kitchen scenes shot at Belvoir Castle, the majority of the elaborate interior sets were built inside the dome-shaped hangar that once housed Howard Hughes' H-4 Hercules aircraft near the Queen Mary in Long Beach, California, at a cost of $8–10 million.

Director Jan de Bont cited the 1961 film The Innocents as a key inspiration for the visual style and cinematography of The Haunting.

Visual effects were completed by Phil Tippett, who had previously worked on the effects for Jurassic Park (1993).

The studio ordered a new ending to be shot after executives felt de Bont's original ending lacked clarity; the revised ending, involving additional shots of the children's spirits, was completed in June 1999 with actors Lili Taylor and Catherine Zeta-Jones returning for reshoots.

A brief romantic scene between Lili Taylor's and Catherine Zeta-Jones's characters was cut from the final film, with Taylor later commenting that it didn't feel very integral to the story.

To secure a PG-13 rating instead of an R from the MPAA, the filmmakers had to trim several scenes because the original cut was deemed 'too tense' by ratings officials, despite containing no foul language, guns, or traditional violence.