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.
Good news for Honduras' murder capital?
Honduran migrants: 'We left because we had to'
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.

Police said it was discovered at Maeve House in the New Lodge area on Monday after a report from a member of the public.
Army bomb disposal experts were called to the scene and the suspected explosives taken away.
The explosives are said to be enough to make three under-car booby-trap bombs.
Det Insp Stuart Griffin said considerable inconvenience had been caused to residents and he thanked them for their co-operation.
"Thankfully these suspected explosives are no longer in the public domain," he added.
The find comes two years after a similar discovery at Maeve House.
Two and a half kilos of the explosive was found in a cupboard at the building in May 2014.
Speaking about the latest seizure, Deputy First Minister Martin McGuinness said he was "hugely relieved and delighted that these explosives have been recovered and made safe".
"I'm disappointed but not surprised that there are still people within our society who believe that they have the right to attempt to point us all back to the past through attempts to kill people," he told the BBC's Good Morning Ulster.

Team GB skier Tim Farr's £5,000 handbike was found after a social media campaign.
It had been sold for £150 at a Cash Converters shop in south London.
Mr Farr, who was a member of the British Disabled Ski team at the Vancouver Paralympics in 2010, thanked people on social media for finding the bike.
On Facebook, he wrote: "Thank you again to all the amazing people, those who I know and don't, who shared my posts in the search of my stolen bike.
"It has been an amazing couple of days and has restored my faith in humanity."
He said his original call for help had been shared more than 3,500 times and that celebrities and MPs had helped with retweets.
The bike was taken from his car parked outside his home near Balham, south-west London, at about 04:00 BST on 21 April.
Police retrieved the bike after being alerted via social media by people who had spotted it in the shop.
More than £1,700 was raised on a crowd funding website to pay for a new bike for the skier.
This money will now be donated to charity.
Firemen in northern Honduras have found the remains of four teenage boys who were kidnapped on 31 January.
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One and a half kilograms of what is believed to be Semtex plastic explosive have been found at a block of flats in north Belfast.
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A paralympian has been reunited with his specially adapted bicycle after it was stolen from outside his home.