Torrential rains began to pelt the Chitral district, in the Khyber Pakhtunkhwa province bordering Afghanistan, on Saturday and continued into the night, residents said.
Maghferat Shah, Chitral district administrator, said some residents were missing after flash floods swamped a local mosque in Drosh town in Upper Chitral.
"The floodwater killed 10 people and caused serious injuries to 21 others at the mosque. Some of them had been swept away in the floodwater and are still missing," he said, according to Reuters.
During the holy month of Ramadan it is common for people to pray at the mosque during night hours.
Shah said 18 people had been killed in other areas due to rain and flash floods, and there were fears the death toll will increase once rescuers reach remote mountainous areas.