It was renamed after the poet Friedrich Schiller who was teaching as professor of philosophy when Jena attracted some of the most influential minds at the turn of the 19th century.

With Karl Leonhard Reinhold, Johann Gottlieb Fichte, G. W. F. Hegel, F. W. J. Schelling and Friedrich Schlegel on its teaching staff, the university was at the centre of the emergence of German idealism and early Romanticism.

Elector John Frederick of Saxony first thought of a plan to establish a university at Jena upon Saale in 1547 while he was being held captive by emperor Charles V. The plan was put into motion by his three sons and, after having obtained a charter from the Emperor Ferdinand I, the university was established on 2 February 1558.

The University of Jena has preserved a historical detention room or Karzer with famous caricatures by Swiss painter Martin Disteli.

During the 20th century, the cooperation between Zeiss corporation and the university brought new prosperity and attention to Jena, resulting in a dramatic increase in funding and enrollment.

The racial researcher and SS-Hauptscharführer Karl Astel was appointed professor in 1933, bypassing traditional qualifications and process; he later became rector of the university in 1939.

A Senate Commission noted the participation of the physician to the "euthanasia" murders of physically or mentally disabled children.

The aim is firstly to give the students the opportunity to visit with relatively few problems at the partner universities and events in order to broaden the range of subjects and topics.

In addition, the cooperation provides the university management the opportunity to share experiences with their regular meetings and initiate common projects.

The co-operation continues at other levels: for example in a joint mentoring program for female postdocs or in the central German archives network.

Jena University is one of the founder of The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, that was founded in 2013.