The boy became ill on Feb. 3 with a cough and other respiratory symptoms, according to the Health Ministry's Web site.
He died a week later in a hospital in the city of Solo, about 280 miles southeast of the capital, Jakarta, said Sumardi, a ministry spokesman. Like he many Indonesians, Sumardi goes by one name.
Tests confirmed the boy had been infected with the dangerous H5N1 strain of the bird flu virus, the ministry's Web site said.
The victim's neighbors had sick chickens on their property and the boy apparently slaughtered some of them before he became ill, the ministry said.
Indonesia has regularly recorded human deaths from bird flu since the virus began ravaging poultry stocks across Asia in 2003.
Bird flu remains hard for people to catch, but health experts worry the virus could mutate into a form that passes easily among humans, sparking a pandemic. So far, most human cases have been linked to contact with infected birds.
Scientists have warned that Indonesia, which has millions of backyard chickens and poor medical facilities, is a potential hot spot for a global bird flu pandemic.
More than 225 people have died worldwide from the virus, according to the World Health Organization.