The girl, from the southern province of Qena, was found to be "very critical" and hospitalised "too late," health ministry spokesman Abdel Rahman Shahin told AFP.
Although the girl had been ill for more than 10 days, she had only been treated with Tamiflu for the past two days, he added.
John Jabbour, a World Health Official in Cairo, had earlier in the week told AFP the girl had been in contact with poultry.
The highly pathogenic virus has killed 15 people out of the 35 cases reported to date in Egypt. The disease was first diagnosed in the country in February 2006.
Egypt's geographical location on major bird migration routes and the widespread practice of keeping domestic fowl near living quarters have led to it being the hardest-hit country outside of Asia.
Women and children have borne the brunt of the virus due to their role in taking care of domestic fowl.
The government says it is conducting a vigorous campaign to combat the spread of the virus through vaccinations and raising awareness, but cases continue to appear.