According to the new list by European zoo expert Anthony D. Sheridan, the eastern German park, which welcomes one million visitors per year, couldn't be beat by facilities in the country's larger cities.
Among other large European zoos, it was surpassed by first-place winner the Vienna Zoo. The third place winner was the Berlin Zoo, home to famous polar bear Knut.
The Cologne Zoo made sixth place, according to the new rankings.
Among smaller zoos that see visitor numbers of around 500,000 per year, France's St. Aignan Zoo topped the list, with zoos in Germany's Osnabrück and Wuppertal taking fifth and ninth place respectively.
Sheridan, an animal conservation specialist and member of the Zoological society of London, plans to present the results in Osnabrück on Thursday. The rankings are based on his analysis of some 80 zoos in 21 European countries.
Criteria included animal welfare, visitor numbers, expenditures, nature protection, admission fees, child friendliness, transportation connections and gastronomic offerings.