The history of the University of Innsbruck starts about 100 years before its official foundation in 1669, when in 1562 a Jesuit school/college was established. Emperor Leopold I used this school as a foundation to establish a university on 15 October, 1669. He guaranteed its financing by introducing a new extraordinary tax on salt extracted in Hall, the so called "Haller Salt Surcharge". Eight years later in 1677, the founding certificate was issued, which mentioned four faculties.

In the following 150 years, the University had to endure challenging times – it was dissolved and reopened twice. In 1826, Francis I Emperor of Austria finally founded the Faculty of Philosophy and the Faculty of Law and, thereafter, other faculties were established step-by-step. In 1969 teaching started at the Faculty of Civil Engineering Sciences and Architecture, and in 1976 the Faculty of Sociology and Economics was established, which used to be integrated into the Faculty of Law and Political Science. Under the University Act 2002 the University was re-organized into 15 faculties and the Faculty of Medicine became a University in its own right – the Medical University of Innsbruck. In 2012 the School of Education has been established and became the 16th faculty of the University of Innsbruck.