The National Disaster Management Authority (NDMA) said 22 people were killed in southern Sindh province and 18 in Balochistan.
Another 15 died in Punjab, 14 in Khyber-Pakhtunkhwa, 12 in the tribal region and three in Pakistan-occupied Kashmir.
The NDMA is leading rescue and relief operations with the help of its provincial chapters. The army has been providing support in the cities of Karachi and Peshawar and parts of Balochistan.
The twin cities of Islamabad and Rawalpindi received heavy rain for the second consecutive day today. Major roads of the capital were inundated and the flow of traffic in early busy hours was slow.
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A total of 104 mm of rain was recorded in Rawalpindi and 96 mm in Islamabad.
A spokesperson of the Meteorological Office told Radio Pakistan that rains would continue intermittently till tomorrow.
Gujrat district of Punjab has received the highest rainfall of 136 mm, he said.