The bus traveling from Banepa to Ghimregaon, Nala, of Banepa overturned while allowing a motorcycles coming from the opposite direction to pass through.
The bus was carrying around 70 passengers, according to Inspector Santosh Tamang of Area Police Office, Banepa.
Two of the deceased have been identified as Sadhuram Ghimire and Ram Gopal Ghimire.
The third passenger who died had not been identified until Friday evening.
Of the injured passengers, 10 have been referred to Tribhuvan University Teaching Hospital and Neuro Hospital in Kathmandu, while 40 are receiving treatment at Sheer Memorial Hospital, Banepa.
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