Edmonton police said Mark Marek, 38, owner of the site, was charged Tuesday night after a "complex" investigation lasting more than a year.
“It is alleged that Marek posted the video online in Edmonton, knowing the video that was sent to him by Luka Magnotta was depicting a real murder,” said Staff Sgt. Bill Clark in a news release.
Edmonton homicide detectives began investigating the website and video in June 2012, following the slaying of Jun Lin in Montreal.
Magnotta, 29, is suspected of killing Jun Lin, a Chinese university student in Montreal, filming and broadcasting the alleged act, and mailing body parts to Canadian political parties.
Marek is in custody and is expected to seek bail Thursday.
More charges may be laid pending further investigations.
Marek has defended his website's role in the case, saying it provides a public service by educating the public about the dangerous side of human nature.
Marek said the video came to him from a contributor on May 25, 2012, and was posted the same day. Marek said that he and most of the site's members felt the video was real.