In its first three weeks in theatrical release in Paris, France, more than 100,000 tickets were sold. According to "Genet: A Biography" (1993) by Edmund White, this was the first time that a film with such a strong gay theme had achieved this kind of box-office success.
The film was selected to screen in competition at the Venice Film Festival in 1982. That year, the Golden Lion for Best Film went to Wim Wenders's Lo stato delle cose (1982). This was much to the disapproval of French director Marcel Carné who withdrew as President of the Jury after releasing the following statement: "I would love to make a personal statement. While being President of the Jury, I would love to express my disappointment in not having been able to convince my colleagues to place R.W. Fassbinder's 'Querelle' among the winners. As a matter of fact, I've found myself alone in defending the movie. Nevertheless, I keep on thinking that, although controversial, R.W. Fassbinder's final movie, want it or not, love it or hate it, will one day find its place in the history of cinema". The statement appears as an introductory prologue at the beginning of the film on DVDs and video-cassettes in Italy.
Initial costume tests of Brad Davis and two other actors in their snug fitting sailor britches were determined to be too revealing for mainstream audiences and so they all wore tight underwear on film afterwards to avoid unsightly bulges. At least one photo from these costumes tests survives as evidence. As things turned out, Davis's personal enthusiasm is still very apparent in several scenes.
Reportedly, the source novelist Jean Genet did not see the film, once saying this was because "you can't smoke at the movies".
According to "Genet: A Biography" (1993) by Edmund White, the film was originally going to be directed by Werner Schroeter but finance couldn't be raised with him as director. Both Sam Peckinpah and John Schlesinger were considered to direct before in the end German filmmaker Rainer Werner Fassbinder was hired to helm the film.