The death occurred last week in the southern province of Aswan, health ministry spokesman Hossam Abdel Ghaffar said.
In the capital, a 42-year-old man was diagnosed and quarantined on December 26, the 25th case of bird flu in the country this year but the first infection reported in Cairo.
Eleven patients have recovered while four remain under observation, Abdel Ghaffar said.
Signup to our newsletter and follow us on Facebook and Twitter!
The H5N1 strain has killed more than 400 people worldwide since it first appeared in 2003, most of them in southeast Asia.
It is one of several deadly or potentially deadly strains of bird flu that are closely monitored by the World Health Organisation.
The strain is different from the H5N8 version, whose spread on European poultry farms this year has prompted WHO calls for vigilance.
A third strain of bird flu -- H7N9 -- has killed more than 170 people since it emerged in 2013.