In the original script, Elliot (Tom Hanks' character) was supposed to fall victim to the killer. However, Hanks was so charismatic onscreen that the writers opted not to film Elliot's murder.
The film's shooting was done in 15 days, and the entire production process, from writing to final cut of the film, was done in four months.
In the DVD commentary, director Armand Mastroianni said that horror fans frequently confuse this film with When a Stranger Calls (1979), because of their similarly threatening titles. Mastroianni also said, 'He Knows You're Alone' and 'When A Stranger Calls' were both playing at a New York City theater at the same time. He said that the theater marquee read 'When A Stranger Calls He Knows You're Alone' as if it was all one big movie title.
According to writer Scott Parker, Tom Rolfing was cast as the killer because Armand Mastroianni liked the intense look of Rolfing's eyes.