The bodies of the victims, aged between 15 and 19, were found in plastic bags by the river Ulua in Yoro province. Their hands had been tied.
The boys were kidnapped by armed men in a village 15 km (9 miles) from where their bodies were found.
It is not clear why the boys - who worked as farm labourers and motorbike taxi drivers in - were abducted.
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The Honduran authorities have not said whether the kidnappers demanded a ransom for their victims, EFE reported.
An average of 11 people are murdered every day in the country, according to official figures.
Neighbouring El Salvador is currently the most deadly country outside a war zone, with almost 100 murders per 100,000 people a year.
Latin America makes up just 8% of the world's population but accounts for nearly a third of all murders.
Firemen in northern Honduras have found the remains of four teenage boys who were kidnapped on 31 January.