Foreign Minister Elmar Mammadyarov announced the request after meeting in Baku with visiting European Union External Affairs Commissioner Benita Ferrero-Waldner. He did not say what aid he had asked for.
Ferrero-Waldner said she would relay the request to the EU's commissioner for sanitation and health, and that the EU would consider what assistance it could provide.
The deadly H5N1 strain of bird flu was discovered in Azerbaijan last week in an area along the Caspian Sea coast near the capital Baku.
No cases of human infections of the disease have been recorded in Azerbaijan.