Director David Koepp, an avid fan of Richard Matheson, decided he wanted his next project to be a horror film and bought a used copy of the 1958 novel A Stir of Echoes, partly inspired by his love of Duel and Matheson's work on The Twilight Zone.

Koepp was terrified when he approached Matheson about his script, worried the changes he'd made to the story would upset the author, but Matheson responded positively, praising Koepp's directorial debut The Trigger Effect and giving his approval.

Koepp cited Roman Polanski's Repulsion and Rosemary's Baby, as well as David Cronenberg's The Dead Zone, as influences on the film.

Principal photography took place entirely in Chicago and lasted 39 days, from October 5 to November 21, 1998, on a $12 million budget.

Director Brian De Palma visited the set and suggested ideas to Koepp, including shooting a long take of Kevin Bacon during the first half of a lengthy dialogue scene.

The hypnosis sequence, in which Bacon's character imagines himself in a theater with everything but the projection screen painted black, was staged exactly as described in Matheson's novel; the theater used was located in Joliet, Illinois.

Bacon's tooth-extraction scene, inspired by a nightmare Koepp had about dying of old age, was achieved practically by blacking out one of Bacon's real teeth and building a removable cap over it, combined with added crunching sound effects and a real tooth palmed and dropped for the close-up.

The film's ghost was filmed at a slow speed of six frames per second to give the spirit an eerie, otherworldly way of moving, a technique praised by critics as an ingenious in-camera special effect.