The album was re-released by EMI as deluxe-edition CD and LP on July 17, 2012. A number of problems were reported with the deluxe release, including it mistakenly using of a different vocal take of "Plume" which was later corrected on digital retail versions of the album, and several digital glitches found throughout the audio on both discs which were not found on the original release. The bonus CD, mastered by Howie Weinberg, was also criticised for suffering from brickwalling.
The CD, LP, and cassette issues were each released with unique cover artwork. The U.S. vinyl release was pressed on amber vinyl, and the first 2,000 copies included a bonus 7" single with "Not Worth Asking" from the original "I Am One" 7", backed with "Honeyspider II". The UK LP has identical artwork to its U.S. counterpart, although the printing is much lighter and the inner sleeve is a heavier stock.
Pisces Iscariot became a quick hit with hardcore fans and casual listeners alike. The album was welcoming to casual listeners mainly due to the cover of Fleetwood Mac's Landslide. This is what made it a mainstream success and radio-friendly. The songs found on Pisces Iscariot and the reissue have a sound very much reminiscent of Siamese Dream and Gish. They range from the soft, pleasant Whir and Landslide to the punk and metal-inspired sounds of Hello Kitty Kat, Pissant and even masterful psychedelic anthems such as the 11-minute fan favorite Starla, the heavy but dreamy Blue, and ballads such as La Dolly Vita and Obscured. The album featured a live cover of The Animals' LSD-inspired tune Girl Named Sandoz. The album was well received by most people who purchased it, and it seemed to have spawned a new cult-following of The Smashing Pumpkins. Pisces Iscariot created a number of fans who sought out more of their rare b-sides, gems, and outtakes, due to the unexpected but unmatchable quality of the ones on this album.