Initially the University - founded as an ordinary academy in 1566 by the initiative of J. Sturm and destroyed during the 1789 Revolution - the Strasburg Faculty was officially established by Consular decree dated Floreal 30 of the year XI in the French Republican calendar (1803), and named "the Protestant Academy of Strasburg". Its task was that of training Lutheran pastors. Though the staff professors proposed new members of the teaching staff, the latter were officially appointed by the Lutheran Church board. In 1808, it was named "the Protestant Seminary".

The Lutheran teaching was of a more traditional nature, fitting easily into the pattern set by the Concordat rules. The innovation was to provide, in connection with Napoleonic reforms, a Reformed teaching along with the traditional one, within the framework of the Faculty of Protestant theology dependent on the University of France.

The studies were gradually organized according to a pattern that was to be adopted by the school of Montauban : five years of study, two of which were preparatory years, and three of theology.

In 1808, it was decided to create a Faculty of Protestant theology in Strasburg for the training of Reformed pastors, since the large-sized Reformed population in Alsace requested that they be represented on the teaching staff as well as at student level. After extensive talks, it was decided in 1818 that the Faculty would be part of the "Seminary", "granting the university faculty members with three chairs in the Seminary" (d'affecter les fonctions de membres de la Faculté à trois chaires du Séminaire). This meant that the titular professors of the Seminary kept their teaching positions and carried on with their classes as in the past. From 1819 onwards, the number of chairs was increased to six, one of which was reserved for a professor of Reformed dogmatics (Mathias Richard, from Mulhouse, held the position until 1868 when he was replaced by Auguste Sabatier). The professors (who were Lutheran) were appointed by the Minister of Public Instruction who selected them among names proposed by the Lutheran board. Their main task was to bestow university degrees.

The School of Theology in Strasburg, whose courses were delivered in German or French, depending on the professors, had distinguished faculty members such as Bruch, Reuss, Fritz, Jung, Schmidt and others.