The music video for the song, directed by Elias Merhige and co-directed by Manson, was filmed sometime during 1996, but remains currently unreleased. It was originally screened at the 1997 San Francisco Film Festival as part of a program titled "Newly Minted Memories". It won a Golden Gate Certificate of Merit in the "Music Video" category. Despite these three known screenings, the video remains absent from all recollections of The Heirophant community, adding to the mystery surrounding it.
In 1996, Merhige was contacted by Marilyn Manson in regards to producing a music video for "Cryptorchid", the day after he saw Merhige's experimental horror film Begotten. Manson and Merhige met in Los Angeles, California where they would produce the "Cryptorchid" video. Merhige also expressed interest in filming a video for "Antichrist Superstar", but wanted to use a bulk of footage outtake that he had already compiled. He shot excess material featuring Manson, then put it together with the pre-existing scenes.
Merhige used military footage from different countries and different wars, that depicted the fascist aspect of the song, but Manson was not quite sure that it represented the criticism that it deserved. It wasn't ultimately Manson's opinion that mattered however because Interscope was appalled by the video. "That's not to say it won't be seen," said Manson, "but I'm not sure if [Merhige] ever had a fair chance of finishing it because of the record company."
Existing knowledge indicates that the music video was 5 minutes and 30 seconds, more or less. It was filmed in black and white, and incorporated footage from Merhige's Begotten, and also of military warfare. Original scenes including Manson were also filmed, although his character role in the video is uncertain. There is a possibility that to consist with the fascist aspect of the song and war scenes compiled for the video, that one of Manson's depictions was not unlike live performances of the song where he would stand dressed formally at a podium, possibly even tearing apart a bible as performances showcased. Henry Rosenthal of San Francisco-based film company Complex Corporation has mentioned his involvement in the production of the video, although according to Manson only he and Merhige were involved. It is not made clear as to whether or not the video was completed however, as Manson himself claimed he, "was not sure if [Merhige] ever had a fair chance of finishing it".
Nearly 13 years after filming "Antichrist Superstar", the video has still not seen proper, or even partial release independently or through Interscope Records as of May 2009, although Manson has expressed interest in releasing it someday. Potential owners of the video are the Complex Corporation in San Francisco, California, Elias Merhige, or even Marilyn Manson.
On June 19, 2010, the music video was leaked on YouTube in its entirety.