The Robert Koch Institute, which monitors the global pandemic in Germany, said the A(H1N1) virus had been found in the blood of the 36-year-old who died in Essen on Friday.
Doctors still had to determine if the patient had died of the flu alone or from a combination of simultaneous infections.
Germany has only been moderately affected by the virus, with nearly 19,900 cases registered.
The World Health Organisation's latest weekly bulletin published Friday said the disease had killed at least 3,917 people in 191 countries since it emerged in April in Mexico.
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