The 24-year-old soldier, identified only by his surname, Shi, became ill in November 2003 and was treated for pneumonia of unknown origin, the Health Ministry said on its Web site.
He died four days later and was suspected of contracting severe acute respiratory syndrome, from which China was just recovering at the time, the official Xinhua News Agency said. The two disease have similar symptoms.
After a fresh battery of tests in July on the man's lungs, tissue and blood samples, "a team of experts has confirmed ... that it was a human case of the H5N1 strain of bird flu," the Health Ministry said.
The case was disclosed in June in a letter by Chinese researchers to the New England Journal of Medicine. It raised concerns about China's ability to track emerging diseases and cooperate with the World Health Organization and other international bodies, the AP reports.
Shi's death came two years before China reported its first bird flu case and as the virus was tearing though Vietnam and Thailand.
Military hospitals, which answer to the secretive People's Liberation Army, figured prominently in China's lengthy delay in reporting the true scale of the spread of SARS in Beijing in the spring of 2003.
China's reluctance to release timely information about the emergence of SARS in late 2002-early 2003 has been criticized by health experts for contributing to the disease's spread.
The H5N1 strain of bird flu has killed least 135 people worldwide since it began ravaging Asian poultry stocks in late 2003.
China reported the first of its 19 human cases in 2005. The country has suffered 12 deaths.