According to Anglican Alliance, thousands of people stormed the compound in Mardan, near Peshawar last week.
They burnt down the church and destroyed the homes of two priests and the headteacher of the church school.
The attackers also looted newly installed computers from the school before setting it on fire.
No one was harmed in the attack but Bishop Humphrey Peters said the damage had been "very severe".
"We will need to rebuild. We are asking for people around the world to keep us in your prayers," he said.
The Moderator of the Church of Pakistan, Most Rev Samuel Azariah told the Anglican Alliance that the attack would be "very damaging" to relations between communities in Pakistan.
“The government and faith leaders in Pakistan have a role to play in educating people that they have the right to protest, but to damage property and terrify people in this way is completely wrong. The government and faith leaders should provide the lead in preventing attacks," he said.