Since its original airing, critics have listed "Clyde Bruckman's Final Repose" among the best "X-Files" episodes. "TV Guide" called it the tenth greatest episode in television history. Review website IGN named it the best standalone "X-Files" episode of the entire series, writing that the episode " is a distinctive episode of the series, mixing a healthy amount of humor [...] with some very nasty business [...] In just 44 minutes, Boyle creates a fully formed character who makes a big impact in his one and only appearance." Topless Robot named it the ninth-funniest episode of the series. Starpulse listed it as the third-best "X-Files" episode. Charlie Jane Anders and Javier Grillo-Marxuach of io9 included it on the list of "10 TV Episodes that Changed Television". Tom Kessenich, in "Examination: An Unauthorized Look at Seasons 6–9 of the X-Files", named the episode the seventh-best installment of the series, noting that it features "a wonderful blend of humor, drama, and pathos, something "The X-Files" did better than just about any other show this past decade." The cast and crew of the series have expressed their enjoyment of the installment. Duchovny considers "Clyde Bruckman's Final Repose" to be one of his favorite episodes of the third season. Nutter highlighted it as one of the most enjoyable entries that he had worked on. He also noted that, "the writing was so tight and so crisp and so fresh that I think, as a director, the only thing you have to do is create the atmosphere, set up the characters, set up the shots and you are basically invisible. Then you step back and just let it happen." Series writer and producer Frank Spotnitz stated that the episode worked on many levels and that it is his favorite of the episodes written for the show by Morgan. In 2016, Ira Madison of Vulture.com named it the best episode of the series and "one of the best episodes of television ever", stating that the episode "takes every element that made the series so iconic and throws them all into one heartbreaking installment".