The two-seater aircraft crashed near Shanti Stupa in Pokhara, killing pilot Stephen Shrestha and a Chinese national, local authorities said.
Shrestha was also the owner of the aircraft.
Chief at the Pokhara Airport Pratapbabu Tiwari said that the reason of the crash was still unclear.
"It was raining lightly and clouds had covered the sky this morning," he said.
Pokhara, the second largest city in Nepal, is a major tourist hub.
Ultra-light aircraft are popular among tourists for sightseeing the Pokhara Valley and the Annapurna mountain range.
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