"Now we need to look for an alternative place to educate these girls," Fidda Draikh, principal of the 160-student school, said.
"We cannot leave them without a school."
The Israeli military had no immediate comment on the Palestinian reports.
'No Hamas ties'
The shuttered medical centre has no ties to Hamas, Dr Hafez al-Sadr, the facility's director, said.
He said though the unit has the same name as the charity, it is run by a different charitable organisation that was controlled by Hamas until the government President Mahmoud Abbas replaced its chief administrator last year.
Though Israel is trying to negotiate a peace deal with the Palestinian Authority (PA), troops also raided Nablus offices of the PA's ministry of religious affairs.
Three weeks ago, Israel and Palestinian militants in Hamas-ruled Gaza agreed to a truce.
But citing confrontations between Israel and Hamas in the West Bank, Gaza fighters have already violated the agreement.