Local Christian officials said a stone church in Tulkarem built 170 years ago was torched before dawn on Sunday.
Another church in the village of Tubas was attacked with firebombs and partially burned.
On Saturday, attackers had hurled firebombs and opened fire at five churches in the West Bank and Gaza, sparking concerns of a widening rift between Palestinian Muslims and Christians.
Ismail Haniya, the Palestinian prime minister, called on Palestinians on Sunday to refrain from sectarian strife.
"All Palestinian citizens must prevent all harm to all Christian churches on Palestinian land. Our Christian brothers are citizens of Palestine. They are Palestinians," he said.
The violence began last week after Pope Benedict, in a talk rejecting religious motivation for violence, cited the words of a Byzantine emperor who characterised some of the teachings of the Prophet Muhammad as "evil and inhuman", particularly "his command to spread by the sword the faith".
The pope has since apologised following massive protests across the Muslim world, including a march by 2,000 people in downtown Gaza City on Friday.
Christians are believed to number about 50,000 people in the West Bank, Gaza and east Jerusalem, about 2 per cent of the Palestinian population.
Bishop Alexious of St Perfidious church, a 1,425 year-old Greek Orthodox Church in Gaza City, said most worshippers stayed home from Sunday services after the church was repeatedly hit by homemade explosives on Friday.
The attacks on the church were the first in recent memory, residents said, and were expected to subside.