"The girl died (Thursday)," said a spokesman from Indonesia's bird flu information centre. "She has been confirmed positive for the virus by two labs."
The 15-year-old girl had been admitted to intensive care in the capital Jakarta and was the sprawling archipelago nation's 93rd confirmed case, the spokesman said, declining to be named.
A 29-year-old man showing bird flu symptoms died Wednesday in Solo, about 500 kilometres (300 miles) from the capital. Tests are being conducted to confirm he had the virus.
Most human infections have occurred after contact with sick birds. The government has banned the popular practice of keeping chickens in backyards in Jakarta to try and curb the disease's spread.
Indonesia had hoped to eradicate human fatalities from the virus this year, but has recorded at least 15 deaths.
The World Health Organisation says the deadly H5N1 strain of bird flu has infected 288 people and killed 170 of them, mostly in Southeast Asia, since 2003.
Scientists say multiple strains of the disease originated in southern China and spread elsewhere.
They worry the virus could mutate into a form easily spread among humans, leading to a global pandemic with the potential to kill millions.
The fear stems from the lessons of past influenza pandemics. One in 1918, just after the end of World War I, killed 20 million people worldwide.