Peter Dalglish, 62, was arrested at his home near Kathmandu last year and was convicted in June of sexually abusing two boys aged 12 and 14.
"He was sentenced to nine years in jail in one case and to seven years in the other," said Thakur Nath Trital, information officer at the court in Kavre district, 30 km (20 miles) east of Kathmandu.
The sentences will run concurrently.
Dalglish, who was present in court for the sentencing on Monday, pleaded not guilty and would appeal, his lawyer said.
"Due process has not been fulfilled during the investigation in the case. So we’ll appeal,” the lawyer, Rahul Chapagain, said.
Dalglish was also been ordered to pay about $9,100 in compensation to the boys, Trital said.
Dalglish had been helping children from poor families in Nepal by providing financial support. He had earlier worked with humanitarian agencies like U.N. Habitat in Afghanistan and a U.N. mission in Liberia, Chapagain said.
Activists said the sentence would help deter other possible offenders in a country with a poor record for crimes involving children."It will help break the belief that Nepal is not serious about child abuse," said Tarak Dhital, an independent activist campaigning for child rights.