Studies of agriculture were established at the Czech Technical University (ČVUT) in 1906, and the first agricultural engineers graduated in 1911. In 1920 the Faculty of Agriculture and Forestry was established, and in 1952 the faculty became an independent institution, University College of Agriculture in Prague (Czech: Vysoká škola zemědělská v Praze; VŠZ). In 1966 it moved to a newly built campus in Prague-Suchdol, where it has been located since.
The Faculty of Forestry, established in 1952, was part of ČVUT until 1959, then a part of the agricultural university until 1964, when it became the independent Institute of Forestry Science (Czech: Vědecký lesnický ústav). It has been a part of ČZU since 1990.
The university adopted its current name in 1995.
From 1952 to 1980 the Masters degree offered by the university lasted five years. It then switched to a four-year course from 1980–90, before switching back to five years. Since 1993 three-year bachelor study has also been available.