The fire caused heavy damage at the offices early Friday, investigators said.
It followed other violent incidents that came after the club signed two Muslim players last month, Haaretz reported.
Asaf Abras, a fire department spokesman, said the heaviest fire damage was in a section of the club where there were trophies and a storage room.
"Some items were collected at the scene and sent to the forensic lab," Abras said. "At this point, we've determined that this was arson."
Prime Minister Binyamin Netanyahu condemned the suspected arson as "shameful" and "racist."
"The Jewish person that has suffered boycotts and expulsions must serve as 'light unto the nations,'" he said.
Four Beitar Jerusalem fans were indicted Thursday on charges including harassment of the Muslim players Gabriel Kadiev and Zaur Sadaev, both from Chechnya.