According to reports, when the bus reached Sabhakhola town in Sankhuwasabha district Saturday night, the five men dragged the woman inside the bus.
The attackers included two teens, aged 17 and 18.
The nun was rescued by an ethnic organisation, the Sanghiya Limbuwan Rajya Parishad, whose members also caught the five men and handed them over to police.
The woman was taken to the local health centre. However, its services proved inadequate and she was taken to the B.P. Koirala Institute of Health Sciences in Dharan.
There was no immediate reaction from Nepal's Buddhist organisations.
Nepal is the birthplace of the Buddha, the founder of Buddhism, and many communities still follow the custom of sending one member of the family to a monastery or nunnery to become a monk or a nun.