Early on Monday, settlers damaged the mosque, located in Qusra village some 15 kilometers southeast of Nablus, when they threw burning tires inside it.
Settlers also broke several of the mosque's windows and threw rocks at Palestinian vehicles.
The Palestinian Authority condemned the attack, saying that the Monday's incident is not the first attack carried out by settlers against mosques in the West Bank.
The incident came after hundreds of Israeli police and soldiers dismantled three homes in the settlement of Migron.
Around 200 settlers tried to stop the bulldozers not to dismantle the buildings.
In early August, the Supreme Court issued an identical order, although it gave the authorities until March 2012 to implement the decision.
Under a "price tag" policy adopted by settlers, they attack Palestinians and their property in response to Tel Aviv's measures against settlements.