It was founded in 1558 by Johann Hoppe (1512–1565), who had previously worked at schools in Kulm and Elbing until Catholic Prince-Bishop Stanislaus Hosius closed them.

Achatius Curaeus (1531–1594), from the University of Wittenberg, was made the first rector, but due to the theological conflicts between Gnesio-Lutherans and Philippists, he soon left.

Along with similar schools in Elbląg and Toruń, the gymnasium transformed the province of Royal Prussia into a center of classical studies in the 16th century.

[3] The university ambitions of the Gymnasium can be proved by the fact that in 1580-1611 the following chairs were created: theology, philosophy, law and history, rhetoric, mathematics, medicine with anatomy, Greek, Hebrew and oriental languages.

In June 2008, the National Museum in Gdańsk unveiled a memorial table dedicated to Academic Gymnasium to mark the 450th anniversary of its founding.