The first reference to the agricultural estate of Čertousy dates back to the year 1322. At that time it was owned by Seiboth of Benešov, a wealthy burgess from Prague. In 1357 Archbishop of Prague, Arnošt of Pardubice, purchased the Estate from Seiboth´s son Henslin for Charles University.
In 1366 the Estate was presented to Charles Collage, newly founded by Emperor Charles IV. This is also stated in its Foundation Charter.
In the 15th century during the Hussite wars the Masters of Charles University lost the ownership rights to Čertousy Estate, however, they purchased it again in 1471 from Jaroš of Trčousi (Čertousy) and this was, with the permission of King George, entered into the Land Register.
After the Battle of the White Mountain in 1620 the Estate was shortly in the possession of Jan Savojský, Vicar General of the Brothers of Mercy. In 1639 during the Thirty Years´War the Estate was burnt out by the Swedes and later within the process of re – Catholicization it was, for a brief period, owned by the Jesuits.
In the 18th century the Estate was rebuilt by the Masters of Charles College under the supervision of builder Kaňka. During the reign of Maria Theresa the Estate was, due to its size, given land-registry number 1. Later the estate belonged under the administration of Michelské Endowment Estates. In 1787 the serfdom was abolished here and the Estate was divided into 8 equal parts which underwent further process of dividing and joining.
In the 19th century some of these parts became the property of several rich citizens of Prague and only in 1879 František Viktor Veselý started to buy the individual of the former Estate. And so by the Decree of the Land Register Committee of the Kingdom of Bohemia issued on 28th April 1900 its former state of 1357 was confirmed and this was entered into the Land Register.
In 1906 the land-registered Estate is bought by Jaroslav Stára of Radonice. He, and later his son Jaroslav, run the place until 1948. In this period new buildings were built and the former ones reconstructed. After the nationalisation by the communist regime in 1948 the place was administrated by Státní statky until 1993. At the time the former 7 buildings of the Estate were demolished, all the wells were covered up and the total demolition of the rest of the Estate and building of new pigsties were considered. These plans were not completed due to the new direction of the social development after 1989.