Eleven other European cities have been nominated for the award, selected among more than 2,400 applications.
Two other Croatian cities applied for the nomination, Djakovo and Slavonski Brod, but a jury eventually selected Zagreb.
An international EFE jury, comprising representatives of 12 AEFP/EFE member countries, will visit Croatia on June 25-27 to evaluate Zagreb for the award.
AEFP promotes culture, tourism and sustainable development.
The 2013 EFE awards - bronze, silver and gold - will be presented in Nieuwpoort, Belgium in mid-September.