The Nowodworski Secondary School was founded in Cracow in 1588 on all the strength of the Jagiellonian University Senate resolution. The aim of the school was to prepare boys for higher education at the university. In 1617 and 1619 funds were given to the school by Bartlomiej Nowodworski, a knight of the Order of Malta. This is why the Maltese Cross became the school's emblem and now every student receives it at the graduation ceremony.

In 1928 the school was named after Bartlomiej Nowodworski. The school always enjoyed a reputation of being one of the best schools not only in Cracow, but in the whole of Poland. Many famous people graduated from it - among them the polish king, Jan III Sobieski. The school was first located where Collegium Novum, the main building of the Jagiellonian University is now located.

In 1898 Jozef Sary designed the new building at Plac Na Groblach 9, the school's present site. The school belongs to the UNESCO Associated School System and organizes a wide range of exchange projects with schools abroad, co-operates with The Stefan Batory Foundation and belongs to the Creative Schools Society and The Oldest Schools Association in Poland.

In 1998 school celebrated the 410th anniversary of its founding, the 100th anniversary of the new building and the 70th anniversary of receiving its new name.

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