Bartłomiej Nowodworski, soldier, philanthropist and Poland's most famous Knight of Malta, bequeathed funds in 1617 and 1619 to the first secular secondary school run by the Kraków Academy, which had existed since 1586.. In 1630, a bequest was also made by Gabriel Prowancjusz Władysławski. These foundations enabled the construction of new premises for the  Nowodworska School. Between 1636 and 1643, Jan Leitner erected a Baroque-Mannerist building reminiscent of the Gothic, which was also subsidised by the rector of the Academy, Jakub Najmanowicz, and King Ladislaus IV.  The school was called the Collegium Władysławsko-Nowodworskie in honour of its founders. It consisted of two parallel pavilions with gabled roofs, connected on two sides by a wall, bound by a cobbled courtyard surrounded on three sides by cloisters.

During the Swedish Deluge, the invaders ransacked the building and made it into a stable. Teaching resumed in 1657, but the Russian army closed the school, converting it into barracks in 1769.  In the 1770s. the building was renovated and the oratory converted into an assembly hall. In the 1840s, the cellars were filled in and bricked up, and the Collegium was repaired in 1845.  In 1855, a third wing designed by Tomasz Majewski was added in a style similar to the older parts of the building. The school moved to new premises in 1898, and the Jagiellonian Library was housed in the building. In 1914, it served as a military hospital. The library reopened in 1916 and took over the entire building after renovations between 1927 and 1932. The building survived the Second World War. Since 1949, it has been occupied by the Medical Academy, i.e., Collegium Medicum ofJagiellonian University.

In 1939, in the courtyard of the Collegium, 19-year-old Karol Wojtyła, later to become Pope John Paul II, made his acting debut in front of Kraków audiences as a student of Polish Studies at the Jagiellonian University. Among others, the school of great educational merit, where lectures were given in Polish and great importance was attached to the study of Polish history and Polish literature, was attended by: Jan Matejko, Stanisław Wyspiański, Stanisław Estreicher, Józef Mehoffer, and Kazimierz Przerwa-Tetmajer.