Fouad Belkacem, the leader of the Sharia4Belgium group, was jailed for 12 years by the court in the city of Antwerp, a spokeswoman for the prosecutor's office, Fabienne Nackaerts, told CNN.
Of the 46 people accused in the case, 36 could not be found and their arrests were ordered in their absence, a news release from the Antwerp court said. Of the 10 who appeared in court, one was acquitted.
Most of those who could not be found are thought to be still fighting in Syria
or to have died there.
Those accused of being leaders in the terror group were sentenced to 10 to 15 years in prison and fines of 24,000 to 30,000 euros ($27,170 to $33,940), the court said.
Those accused of active membership of Sharia4Belgium without leadership roles were given lesser sentences.
The offenses were committed in Antwerp and Brussels in Belgium as well as in Syria and Turkey between 2010 and 2014, the court said.
The court "also established that Sharia4Belgium has played an active role in the departure of several Syria fighters," it said.
Radical British preacher Anjem Choudary's name was mentioned several times by the prosecutor during the Antwerp trial as having helped Belkacem set up Sharia4Belgium.
Choudary acknowledged to CNN that Belkacem had consulted with him in 2010 on establishing the group, whose name refers to Sharia, or Islamic, law.
Speaking after the sentence Wednesday, Choudary said: "I believe nowadays in Europe if you call for Sharia you are considered to be guilty. Abu Imran (an alias for Belkacem) was just doing his Islamic responsibility.
"In 2010 he came to see me and he asked about how to set up a branch of our own body that we had in Britain. Sharia4 Belgium was under our own guidance. Abu Imran helped set up branches in Holland and France.
"I am extremely proud and I love Abu Imran and all the members of Sharia4Belgium."
Choudary, who was a co-founder of the banned UK Islamist group Al Muhajiroun, told CNN last August that he believed the ISIS extremist group
would spread rapidly and be in Europe and the United States within decades.
As of September, 350 Belgian citizens were known to have traveled to Syria and Iraq
to join Islamist extremist groups fighting there, the Belgian Interior Ministry said then.
Given Belgium's relatively small Muslim population, this is a high number, compared with other European nations that have seen radicalized citizens head overseas to fight.
Authorities fear some who return will seek to carry out attacks motivated by jihadist ideas.
Belgian authorities last month carried out a series of counter-terror raids on a suspected jihadist cell amid fears that its members were plotting an imminent attack on Belgian soil. A federal prosecutor said they planned to target police officers.