The girl from Karawang district in western Java died on July 3, three weeks after visiting a market and helping to carry slaughtered birds home, according to the Indonesian Health Ministry's website.
Indonesia is the nation hardest-hit by bird flu, with 157 other fatalities reported since 2003 out of 357 worldwide, according to the most recent World Health Organisation figures, which exclude the latest death.
Meanwhile, on Thursday Hong Kong closed a popular tourist spot where hundreds of caged birds are on display after the deadly H5N1 avian flu virus was detected at one of the stalls.
The agriculture, fisheries and conservation department said it was closing the Yuen Po Street bird market in the city's bustling Mongkok district for 21 days. There are about 70 bird stalls in the market.
The move came after the virus was found in a swab sample collected from a cage holding an oriental magpie robin during a routine avian influenza surveillance operation.
All the stall's birds would be killed, the department said in a statement.
A spokeswoman said they were still investigating the cause of the virus as the bird itself was not infected.
The risk of transmission between pet birds and humans is "relatively low", the Hong Kong Centre for Health Protection head Thomas Tsang told a news conference after the closure was announced.
The southern Chinese city occasionally finds bird flu in poultry but there have been no major outbreaks since 1997, when six people died from a mutated form of the virus. Millions of birds were then culled.
In June, Hong Kong reported its first human case of the H5N1 in 18 months when a two year-old boy from the neighbouring province of Guangdong who traveled to the city for medical treatment came down with the illness.
The virus has killed more than 330 people around the world, with Indonesia the worst-hit country, suffering eight fatal cases this year. Most human infections are the result of direct contact with infected birds.
The former British colony is particularly nervous about infectious diseases after an outbreak of the deadly respiratory disease SARS in 2003 killed 300 people in the city.