The epicentre was near the Nepalese municipality of Dipayal, 340 kilometres (210 miles) west of Kathmandu at a depth of 15 km at around 2:00 am (2030 GMT), according to the US Geological Survey.
Six people died in the western district of Doti, including three members of the same family, local police chief Rajendra Dhamala said.
Five others were injured and were undergoing treatment at a local hospital.
Some houses were damaged and local authorities said they were still assessing damages and casualties.
Tremors were felt in northern India but there were no reports of deaths or damage there.
Residents of Indian capital New Delhi posted videos on social media including swaying light fixtures and shaking fences.
The Indian National Center for Seismology reported the quake as magnitude 6.3.
Western Nepal was also jolted Wednesday at around 9:00 pm (1530 GMT) by a magnitude 4.8 earthquake at a depth of 10 km.
Nearly 9,000 people died when a 7.8-magnitude quake struck Nepal in April 2015, destroying more than half a million homes.
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