The boy died on Thursday in Dong Thap province after being hospitalised with a high fever, the provincial health department said. Test results at the Pasteur Institute in Ho Chi Minh City revealed he died from H5N1.
He is believed to have contracted the virus from a chicken his grandmother bought and slaughtered in late March.
There have been 123 confirmed human H5N1 infections and 61 deaths in Vietnam since the virus first appeared in the country in 2003, according to World Health Organisation. The last reported case was in February 2012.
The virus can be passed to humans who come in contact with uncooked poultry or poultry faeces.
Vietnam has so far reported no cases of H7N9, a new strain of bird-flu virus, which has reportedly killed seven people in China.
Meanwhile, Cambodia is battling a spike in the H5N1 strain that is baffling experts a decade after a major outbreak began in Asia.
Bird flu has killed eight people so far this year in Cambodia, including six children, while more than 13,000 chickens have been culled or died from the highly contagious illness. The impoverished kingdom is also nervously watching the spread in China of a new H7N9 strain that had not previously been transmitted from birds to humans, but has now killed seven people in China since February.
"We're monitoring it. We're constantly on alert," Sok Touch, head of the Cambodian health ministry's disease surveillance bureau, said of the new virus.
So far Cambodia has not recorded any human cases of H7N9 and is focused on fighting the more common H5N1 virus, which has killed more than 370 people globally since 2003, according to the World Health Organisation (WHO).
The WHO says H5N1 carries a mortality rate among humans of around 60 per cent.
The current outbreak is Cambodia's worst ever, accounting for nearly a third of its 27 human deaths from H5N1 since the virus emerged in the kingdom in 2005 following a spate of deaths in China and elsewhere in Southeast Asia that sparked international concern.
No scientific explanation has been found yet to explain the sharp rise in human victims this year. In 2012, three people died from H5N1 in Cambodia.
"There are some missing pieces in the puzzle and that's why we are looking to see how this can be improved," said Lotfi Allal, an animal expert at the UN Food and Agriculture Organisation in Cambodia.