Those killed included at least 37 people in the eastern mountain district of Illam, where whole villages were swept away by landslides, Nepal's National Disaster Risk Reduction and Management Authority said.
Several other people are still missing.
Heavy rainfall was reported since Friday in the district, which borders India and is known for growing tea.
Six people in the same family were killed when a landslide crushed their home while they slept, Illam's assistant administrative officer Bholanath Guragai said.
Rainfall was hampering efforts to reach the villages and many roads were swept away or blocked by the landslides.
The government said helicopters were also transporting people needing medical evacuations and ground troops were helping move people to safer areas.
One more person was killed in landslide in a neighbouring district.
Three people in another district were killed as they were struck by lightning while three more people died in flooding in southern Nepal.
Nepal's government issued a severe rainfall warning in the eastern and central parts of the country from Saturday to Monday while shutting down major highways.
All domestic flights were grounded on Saturday by aviation authorities because of heavy rainfall and poor visibility but were reopened on Sunday.
The major highways connecting the capital Kathmandu with other areas were closed by the authorities as some parts were blocked by landslides and others were shut as a precautionary measure.
By Sunday evening, one route was partially opened for traffic.
The blockage of roads and transport came as hundreds of thousands of people were returning to Kathmandu after celebrating Dashain, the biggest festival in the Himalayan country.
Thursday was the main day of the two-week festival when people travel to their home villages to be with their families.
Highways were clogged with vehicles on Sunday as the government assessed the situation.
In Kathmandu, some areas near the river were flooded but no major damage or casualties were reported.
The government had declared a public holiday until Monday because of the heavy rainfall.
Flooding and landslides last year around the same time killed 224 people and left 158 injured.
Neighbouring India, which surrounds landlocked Nepal on three sides, has offered to help.
Indian Prime Minister Narendra Modi said on social platform X that the loss of lives and damage caused by heavy rains in Nepal are distressing.
"We stand with the people and Government of Nepal in this difficult time," he said.
"As a friendly neighbour and first responder, India remains committed to providing any assistance that may be required."
The weekend's heavy rainfall arrived at the end of Nepal's monsoon season, which usually begins in June and ends by mid-September.
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