Jewish community officials said it was not immediately clear whether it was an anti-Semitic attack, although the building had been the target of petrol bombers in 2010.
The wife and two children of the synagogue's caretaker suffered slight smoke inhalation in the fire on the top floor of the building, where they lived, said a fire department spokesman quoted by the Belgian media.
The caretaker was absent at the time.
Laurens Dumont, a spokesman for the city prosecutor, said "it would seem that the fire was set deliberately" at the synagogue in the neighbourhood of Anderlecht near the main train station, but the investigation was in its early stages.
The city prosecutor's office said in a statement later "there was no reason to suggest that it was a terrorist attack," months after four people were shot dead at the Jewish museum here in an apparent Islamist militant attack.
The fire department spokesman said arsonists started the fire in the fourth floor of the synagogue in the early hours today.
An official from the neighbourhood's Jewish community, Jehuda Guttman, told Belgian media he did not know for now whether the event was anti-Semitic.
"If this act had been anti-Semitic, the perpetrators would have burned the Torah, sacred books. And that's not the case. I can only guess. Here, we live in peace with everyone," he said.
Mehdi Nemmouche, a Frenchman of Algerian descent allegedly aligned to the jihadist Islamic State, is being held in Belgium suspected of carrying out the murders.
He was arrested six days after the shooting in the southern French port of Marseille and later extradited to Belgium.
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