Allmusic critic Sean Westergaard wrote "... there is a tremendous amount of stylistic diversity here, from the very traditional sound of Julian Kytasty to the very untraditional sounds of Fantômas. In fact, listeners more familiar with The Circle Maker or Bar Kokhba might not be prepared for some of the hard rock treatments of some of these tunes... The Zorn crowd tends to follow his every move and usually know what to expect; the uninitiated should probably approach this one with some caution."
Dominique Leone was positive about the disc as a whole, writing: "...for the most part Zorn's music has yet again proved to withstand the test of time and interpretation. If Masada does indeed go down as his greatest moment, it will be in part because other musicians have run with his ideas and been able to make their own artistic marks with his music. In that sense, The Unknown Masada and the other anniversary series albums are as significant as any release in his canon."