The garden traces back to 1535 when medicinal plants were first grown by Leonhart Fuchs (1501-1566) beside the Nonnenhaus (House of the Nuns), which still exists.
In 1663 a Hortus medicus was created by direction of Eberhard III, Duke of Württemberg (1614–74), with university gardener appointed in 1666.
In 1804 a new garden was established by decree of King Frederick of Württemberg (1754-1816) under the leadership of Professor Carl Friedrich Kielmeyer (1765-1844), which grew and flourished throughout the first half of the nineteenth century.
By 1809 it contained four greenhouses and a lecture hall, with its first seed catalog published in 1820, and from 1818-1825 its plants were reorganized according to the system of Antoine Laurent de Jussieu.
In 1969, the university established a new botanical garden, the Botanischer Garten der Universität Tübingen.