At least half a dozen were injured in the disaster triggered by incessant rains, said Nepal's Ministry of Home Affairs (MHA).
Ministry spokesperson Shanker Prasad Koirala said that according to the data available until Thursday morning, at least 39 people have lost their lives and 18 went missing during the recent floods and landslide.
According to Koirala, the western part of Nepal is severely hit by the floods and landslips, and most casualties were in that area.
As many as 122 houses were swept away by Mahakali river, which is known as Sarada in India, in Darchula district alone.
On Thursday, media reports suggested that at least six Nepali youths from Jajarkot district of western Nepal have been swept away by flood. They were heading to India for employment after completing their college examination.
This time, Nepal's western part that has border with Indian state of Uttarakhand is severely hit.