It was opened in 1931 with the goal to "advance the study of zoology, protect wildlife, and educate the public" in the district of Troja in the north of Prague.

[7] The zoo has contributed significantly to saving Przewalski's horse; for many years, it was the leading breeder of the subspecies.

[8] The idea for a zoological garden in Prague was first proposed in 1881 in a newspaper article by Count Sweerts-Spork, on the occasion of the marriage of Crown Prince Rudolf of Austria and Princess Stéphanie of Belgium.

Under his leadership, the zoo achieved some world-class successes in the area of breeding and scientific research.

A large part of the zoo was flooded and 134 animals died, including an elephant, a lion, a gorilla, and four hippopotamuses.

In 2011 Moja, a western gorilla famous from the multimedia project The Revealed, was moved to Cabarceno Natural Park in Spain.

The birth gives hope that the creature can be rescued from its current status on the endangered species list.