Mark Marek, who operates bestgore.com, faces one count of corrupting morals.
Edmonton police allege Magnotta sent Marek the video last year and Marek posted it online while knowing that it depicted a real killing.
Magnotta is to stand trial in September 2014 for the murder and dismemberment of Chinese university student Jun Lin in Montreal last year. Parts of Lin's body were mailed across Canada in a gruesome killing that made headlines around the world. Magnotta has pleaded not guilty in that case.
Marek, who remains in custody, appeared briefly in court Wednesday and was scheduled to make another appearance Thursday.
Before he was charged, a statement that appeared on the 38-year-old's website said he was going to meet with police for an interview and expected he might be arrested.
"It may sound strange, but at this point in my life, jail doesn't sound all that unattractive," said the statement. "I wouldn't mind taking a break from the world ... I've dedicated my life to fight against Evil and Lies, and I know that God and Truth are on my side.
"I do not fear the servants of Satan. One way or another, my life will end one day, and so will theirs."
Staff Sgt. Bill Clark with the Edmonton homicide unit said the investigation was long and complex because Marek was "very elusive," with no home address and had been out of the country.
He doesn't believe Edmonton police have ever laid such a charge before. It carries a maximum two-year prison term.
Clark said investigators didn't originally have the evidence they needed to charge Marek. The staff sergeant explained that police needed evidence of three things before they could do so: that Marek knowingly and willingly posted the video, that he did so while in Canada and that he was the site's owner and operator at the time.
Last week, Marek landed in Vancouver. Officers with the Canada Border Services Agency seized his computer equipment at the airport and notified Edmonton police. He was then allowed to continue his flight to the Alberta capital.
Clark said police kept in touch with him over the following days by email. He wasn't living anywhere other than in his car. Still needing evidence to build a case, investigators asked Marek if he would be interviewed. He agreed to come in for an interview Tuesday and police charged him after that.
"I can say that he's a very different individual. He has some thoughts that a lot of our investigators were shaking their heads at."
The website opens with a content warning and advertises that it is for adults only. "Videos and images posted on Best Gore are bloody, gut wrenching, teeth grinding, offensive and upsetting. Just as the life itself," it says. "Best Gore exposes the truth about the humans as a whole and the truth is not always nice."
The website also says it has been reviewed by both Canadian and U.S. lawyers and is "100% legal in both jurisdictions."
In May 2012, the site posted a video titled "1 Lunatic 1 Ice Pick.'' It showed a naked man tied to a bed in a dimly lit room. Another man wearing a dark hoodie stabbed the individual and a series of edits showed the body eventually dismembered.
The video stayed online for eight days. After Magnotta's arrest, Marek told The Canadian Press in an email that he removed the video once police identified Magnotta as a suspect.
Clark said the investigation into Marek and his website began at that time but it was difficult to track him down. Officers contacted government and private agencies and businesses, but all had Marek listed with just an Edmonton post office box.
It took investigators until February to find him, but police still didn't have enough evidence to lay charges, Clark said. Marek then travelled to Hong Kong and police put out alerts trying to locate him.
He updated his website regularly while on the road, said Clark.
Officers have flown to Vancouver with warrants for Marek's computer equipment. Clark said the suspect could face additional charges, including hate crime offences, related to other items posted on the website.
He described the site as racist and disturbing, with "violence above and beyond anything normal." It's also unsettlingly popular, with as many as 10 million viewers, said Clark.
He said he doesn't think police have the authority to shut down the website unless Marek is convicted in court.