Blood tests revealed the presence of the deadly H5N1 strain in Abdullah Nagy Amran from Egypt's second-largest city of Alexandria. The boy, aged two years and eight months, is believed to have contracted the virus after coming into contact with dead poultry.
Amran, who is in stable condition, is being treated with the anti-viral drug Tamiflu.
Five cases of bird flu have been registered in Egypt this year, none of them were fatal. Twenty three people have officially died from bird flu since records began in 2006.
As of March 2, a total of 409 bird flu cases have been registered worldwide since the virus was first detected in 2003, resulting in 256 deaths, according to the WHO.
Although there have been no incidences of human to human infection, experts fear that the bird flu virus may mutate into a form that could be easily transmitted from person to person, causing a global pandemic.