The 23-year old woman and her two children are awaiting the chance to return to Belgium from the Al-Roj refugee camp in an area of northeastern Syria that is under Kurdish control.
The Brussels Court of First Instance said Belgium would start facing a daily fine if the woman was not repatriated in the time it set.
The European Union created a common counter-terrorism register in September, hoping to facilitate prosecutions and convictions of suspected militants and people returning home from fighting with Islamic State in Iraq and Syria.
The move was partly aimed at addressing concerns about the fate of hundreds of EU citizens who fought for Islamic State and are now detained in Iraq and Syria.
Many of them could return to Europe and not face trial because of a lack of evidence against them, a factor that has contributed to unease in several EU countries over returning fighters.
The EU security commissioner, Julian King, told Reuters last month that at least 1,300 EU citizens, more than half children, were held in Syria and Iraq.
President Donald Trump, who announced on Oct. 6 that U.S. forces would withdraw from northeastern Syria, has called for European countries to repatriate nationals who went to fight in Syria for Islamic State and put them on trial.