The garden was established on 1 December 1961 as a subordinate institution of the Academy of Sciences of the Estonian SSR and was developed over the following years.

[2] Originally, the main focus of research was the foreign species in Estonian context e.g. plant growth requirements and acclimatisation.

From the 1970s research moved to the use of indigenous plant species in landscaping and horticulture (Ülle Kukk, Vaike Paju, Marianna Saar etc.)

The Botanic Garden has added a number of sections, such as the Audaku experimental station in Viidumäe Nature Reserve on Saaremaa (since 1963) and an arboretum in Iru (1973–1994).

The territory of Tallinn Botanic garden occupy the land of the former farm of Konstantin Päts, the first President of Estonia.