It said the child died in a hospital in Hanoi but gave no gender. Doctors were testing to see if the H5N1 bird flu virus was the killer, the ministry official was quoted as saying.
Vietnam last reported outbreaks among poultry in October, but Son La was not on the government's bird flu watchlist.
The H5N1 virus killed four of the seven Vietnamese who have caught it this year, taking the country's death toll since late 2003 to 46. The last death was reported in August.
Health officials had worried that winter in northern Vietnam might trigger a new wave of outbreaks among poultry as the virus seems to thrive best in cool temperature.
The Agriculture Ministry said 63 of Vietnam's 64 provinces had been vaccinating birds against the virus this year.
The H5N1 virus remains mainly a virus of birds, but experts fear it could mutate into a form easily transmitted from person to person and sweep the world, killing millions.
Globally, the H5N1 virus has killed 209 people out of 340 known cases and most of the deaths are in Indonesia, followed by Vietnam, World Health Organisation figures show. Hundreds of millions of birds have died or been slaughtered.
(Reporting by Ho Binh Minh; Editing by Michael Battye and Sanjeev Miglani)