This is the only episode of the series to have been directed by regular Star Trek director Winrich Kolbe and was the final Star Trek episode directed by him.
When Captain Archer is using the visual sensor array to communicate with the aliens, the sound effects engineers used a modulation device called a Flanger to create the swirling effect of Archer's voice.
Mark Latrelle's contention that Reed dislikes fish is later disproved by a scene in Shuttlepod One (2002), in which Reed's first choice of emergency ration is sea bass.
The mysterious ship that attacks Enterprise in this episode is of the same configuration as the numerous Kovaalan ships that later attack Enterprise in a subspace corridor in E² (2004). However, these similarities are probably unintentional, a result of the digital ship model for 'Silent Enemy' being recycled for 'E²', a frequently used cost-saving measure on the show. Nevertheless, the Star Trek Encyclopedia lists the ship from this episode of potentially Kovaalan origin, even though this may not have been the writers' intention.
The plan view of the alien "stealth ship" is a close copy of the plan view of the Lockheed F-117A Nighthawk stealth fighter.