He was the son of Johann Nicolaus Stupanus (1542–1621), Professor of Theoretical Medicine at the University of Basel, and his second wife, Katharina Iselin.

After visiting well-known Universities in Germany, France and Italy he was awarded the degree of Medical Doctor from Basel under Petrus Ryff, in 1613.

[4] He also took classes in Ancient Greek from Jacob Zwinger, philosophy from Heinrich Justus, and rhetoric from Friedrich Castellio.

[5] On March 28, 1620, he delivered his Inaugural Lecture De fraudibus Paracelsistarum, in which he expressed his opinion about Paracelsus.

Between the two them, Emmanuel Stupanus and his father occupied the Chair of Theoretical Medicine for a total of 72 years.