He was also enrolled at the Rijksakademie, and took courses in classical archaeology from Reinhard Kekulé von Stradonitz, at the University of Bonn.
In 1885, he obtained his PhD (cum laude) for his thesis The Gorgon, which was sponsored by the art historian, Allard Pierson, and published by R. Kröber-Bakels of Amstelveen.
In 1896, he received a special appointment as Professor of aesthetics and art history at the university; succeeding his former mentor, Pierson.
Two years later, during a visit by Kaiser Wilhelm II, he was named a Knight (2nd Class) in the Order of the Crown of Prussia.
Four years before his death, he established the Six Foundation, to sort and maintain his large collection of books and antique objects; including a portrait of his ancestor, the Mayor of Amsterdam, also named Jan Six, painted by Rembrandt.