The boy, who tested positive for the H5N1 virus, died in a hospital here at 7:30 am (0030 GMT), said Nirwan, a staffer on duty at the health ministry's bird flu information centre.
"Medical doctors at the hospital were meeting to discuss his case, since he showed great improvement in his health condition, with his white-blood cell count rising, but the boy suddenly died at 7:30 this morning," said Nirwan.
Results of two tests on blood and saliva samples taken from the boy on Thursday showed he was infected by the deadly H5N1 strain, making him the country's 109th confirmed human bird flu infection case, of which 88 have died.
The boy, only identified by his initials IR, first showed symptoms of bird flu on September 30 but was only admitted to hospital in Tangerang, just west of here, on October 8.
He was transferred to Persahabatan Hospital in Jakarta a day later.
Two tests, usually of samples of blood and tissue, must come back positive for the virus before a victim is confirmed as infected in Indonesia, where the death toll of 88 from avian influenza is the highest in the world.
"The boy had a history of contact with a dead infected chicken near his school," Nirwan said.
H5N1 is widespread in poultry across Indonesia's sprawling archipelago.
Bird flu is usually transmitted directly from infected birds -- typically poultry -- to humans. However, scientists fear that the virus could eventually mutate into a form easily transmissible between people, triggering a global pandemic.
The World Health Organisation announced earlier this month worldwide human deaths from bird flu had reached 201. Besides Indonesia, deaths were recorded in Azerbaijan, Cambodia, China, Egypt, Iraq, Laos, Nigeria, Thailand, Turkey and Vietnam.
Indonesia has been sharply criticised for being slow to act in its fight to control bird flu, which has spread easily in a nation where many people keep chickens and other birds in their backyards and homes.
It was also dressed down after it stopped sending samples of the virus to the World Health Organisation, saying it wanted a guarantee of affordable medicines to treat sufferers before it did so.
The health ministry reverted however to sharing samples again last month.