The boy, a resident of the Banten province in the western part of the island of Java, was hospitalized last week with a high fever and breathing difficulties, which later were confirmed as symptoms of the deadly H5N1 strain of the bird flu virus, the Antara agency said.
Indonesia is the world leader in the number of human bird flu cases, with the highest mortality rate - about 80% - and the disease spreading rapidly among citizens of the fourth most populous country in the world.
The latest fatality brings the death toll from bird flu in Indonesia to 81 out of 102 cases.
According to the World Health Organization (WHO), bird flu has killed 192 people around the world since late 2003. The second hardest-hit country after Indonesia is Vietnam, where 95 human bird flu cases have been registered, with 42 deaths.
