The incident comes amid growing tensions in Jerusalem between the two communities that started before the 50-day bloody war in Gaza and has continued unabated despite heightened security arrangements.
The fire broke out at the playground in the school yesterday evening and was extinguished by emergency crews.
Police and fire services said that they suspected arson based on the visible evidence found at the scene.
The Max Rayne Hand in Hand Jerusalem School is the country's largest Jewish-Arab institution.
Over the past few months, the school has been repeatedly targeted by right-wingers, who have sprayed racist graffiti against Arabs on its walls, local media reports said.
"Even if they manage to dirty the school's walls, they will not manage to bring down our enterprise [of civil cooperation]," Hand in Hand Executive Director, Shuli Dichter, said in a statement.
"In addition to denouncing [these actions] expressing support, we invite the entire Israeli public to join us in the building of Jewish-Arab civil partnership in Israel.
Jerusalem's Mayor, Nir Barkat, condemned the incident saying, "We will not allow pyromaniacs and criminals who take the law into their own hands to disrupt our daily lives".
"We will continue to denounce the extremists and do whatever it takes to restore the quiet to Jerusalem," he said.
The bloodiest war between the two sides broke out after the Hamas fired dozens of rockets at Israel after Israel rounded up its activists in the West Bank following the murder of three Israeli teens there.
