Up to 600 pupils and students were enrolled at the Jesuit College of Lucerne in the 17th century; the majority came from Lucerne itself, and many others from neighbouring regions. Although only young men were allowed to study and women were excluded, the school experienced its heyday in this epoch. Given that the city only had about 4000 inhabitants at that time, the number of 600 students was significant.

For graduates of the grammar school, a continuing offer of higher education had existed since 1600. Gradually professorships were also established: three for philosophy and four for theology. To crown all this, the government wanted to establish a proper, modern academy. In 1647, the government requested authory from Rome  for the Lucerne Jesuit College   to award academic degrees on all levels and even the emperor in Vienna was to be won over to the project! All the necessary foundations were thus already laid – but the project failed, practically at the very last moment. The reason was a comparatively banal legal problem: namely, which ecclesiastical authority should have the right to supervise and inspect. Should it be the Provincial of the Jesuits? Or should it be the Nuncio, who as permanent ambassador of the Pope, had his seat in Lucerne. An external authority was necessary to ensure recognition of the degrees abroad; it was thus a quality assurance measure, comparable with the accreditation practice valid today. Because no agreement was reached, the project failed. In retrospect, this was an almost historic moment, as the first opportunity to lay the foundations of a university in Lucerne had been missed. The Higher Secondary Institution with its grammar school and courses in philosophy and theology thus remained as it was.

It took two hundred years before an expansion towards a university returned to the agenda. Lucerne was once again at the centre of ideological and political polarisation. In the 1830s, rifts opened up between the large liberal and conservative blocs. While the conservatives  wanted to return to a time before the Enlightenment and the French Revolution, the liberals were transforming Switzerland into a modern bourgeois state. After a conservative election victory in Lucerne in 1841, a political dismantling began. This included the renewed transfer of professorships from the Lucerne Higher Secondary Institution to Jesuits. This highly controversial and particularly symbolic step was a beacon for the whole of Switzerland, because the Jesuits were considered the ultimate  in political reactionism and confessionalism. Their appointment triggered a chain of events which finally led to the ‘Sonderbund’ war.

Despite all the resistance, including from within its own canton, the Lucerne government stayed its course. It also sought to consolidate its conservative profile culturally. To provide a counterweight to the new universities of Zurich and Berne, Lucerne founded the ‘Academy of St. Charles Borromeo’. This new Academy accepted prominent conservative exponents as members, published a scholarly journal and planned a large series of events for the winter of 1847/48. Soon the intention to expand towards a university was added. To this end, the plan was, in all seriousness, to benefit from the imminent speratist war. Not only did the government believe that victory was certain, they equally firmly expected that there would be reparation payments, from which they would reserve one million Swiss francs as endowment capital for the university. The Catholic defeat at the end of November 1847 ruined such lofty plans at a stroke and the conservative government and Jesuits were driven out of Lucerne. The return to a premodern order was off the table; the way was paved for the founding of the federal state that still exists today. For the second time though, a project to establish a university in Lucerne had failed.