Homes were submerged or crushed by rocks swept into them by landslides.
At least 88 people died in Nepal and 55 in Uttarakhand, including five from a single family, with dozens more missing in both nations.
Rains further south in India's Kerala state also triggered deadly floods, leaving another 42 dead there.
In Nepal the victims included a family of six, among them three children, whose house was buried in a sudden deluge of soil and debris.
The worst-affected areas are Panchthar district in east Nepal, and Ilam and Doti in west Nepal.
Rescuers were struggling to reach 60 people stranded for two days in the village of Seti in west Nepal, Reuters reported.
Nepal's government is giving $1,700 (£1,220) to the families of each victim of the floods.
In the Himalayan state of Uttarakhand schools have been closed and religious and tourist activities suspended.
The Ganges burst its bank in Rishikesh and the popular Nainital region was severely affected.
Uttarakhand, which normally sees up to 30.5mm (1.2in) of rain for the whole of October, recorded 328mm in a 24-hour period this week.
But the Indian Meteorological Department says the rainfall is now easing.
