Robert Taylor at AllMusic gave The Spectre Within two stars out of five, saying that "Metal fans may enjoy this more than Night on Bröcken, especially "Pirates of the Underground" and "The Apparition," but there is very little, if anything, for the progressive fan." Trey Spencer at Sputnikmusic gave the album a similarly lukewarm review, deeming it "for die-hard fans only". Some criticism was directed at John Arch's vocals, which were described as "slightly irritating due to the unchanging high-pitched nature of his voice", as well as the dated riffs and production. For new fans of Fates Warning, Spencer instead recommended Awaken the Guardian as a better starting point.
In contrast, Jeff Wagner in his Mean Deviation (2010: 56) book wrote that The Spectre Within "set Fates Warning apart from just about everyone else in the metal underground, although parallels could be drawn to Danish band Mercyful Fate, an early influence on [guitarist Jim Matheos]". Wagner also stressed that the album was "darker and more complex than even Iron Maiden or Queensrÿche, and it handled its fantasy imagery intelligently, passing over the clichéd traps of wizards, dragons, and ham-fisted, second-rate riffs".