The federal migration office announced that Mohammed Al Arifii was banned from entering Switzerland or the Schengen area.
The preacher, whose planned visit to the conference had raised objections from critics who accused him of preaching violence and hatred.
He has been accused of anti-Semitism, insulting homosexuals and offering advice on wife-beating, among a range of condemnations.
Federal officials earlier this week ordered the cleric’s name to be removed from the list of speakers at the conference organized by the Central Islamic Swiss Council (CCIS).
Arifi’s appearance in Fribourg was approved last month by the prefect of the Sarine, Carl-Alex Ridoré, who issued directives calling for the meeting to abide by Swiss laws.
The federal migration office did not give reasons for banning the preacher.
The CCIS last year drew 1,500 people to its first conference in Bienne, which was held without incident.