The highest toll was recorded in the province of Khyber Pakhtunkhwa that borders Afghanistan, where 10 children were among 21 killed.
The disaster management authority said 14 of those victims died in the Swat Valley, where media reported a flash flood swept away families on a riverbank.
In Pakistan's most populous province of Punjab, along the frontier with India, 13 fatalities have been recorded since Wednesday.
Eight of them were children who died when walls or roofs collapsed during heavy rain, while the adults were killed in flash floods.
Eleven other deaths related to the monsoon downpours were recorded in Sindh and Balochistan provinces.
The national meteorological service warned that the risk of heavy rain and possible flash floods will remain high until at least Saturday.
Last month, at least 32 people were killed in severe storms in the South Asian nation, which experienced several extreme weather events in the spring, including strong hailstorms.
Pakistan is one of the world's most vulnerable countries to the effects of climate change, and its 240 million residents are facing extreme weather events with increasing frequency.
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