The earliest documents proving the existence of a medieval monastic school at Melk Abbey are a parish register and some parchment scraps dating back to about 1140 and 1160 respectively.

In the 15th century, alongside the Melk Reform strongly influencing Austrian and Bavarian Benedictine religious life, the school flourished and gained reputation.

So, for instance, in 1446 a monk called Simon wrote an education book for six-year-old King Ladislaus the Posthumous of Hungary.

However, starting from around 1530 and mainly caused by the onset of the Protestant Reformation in the Habsburg Empire, the abbey suffered from a dramatic lack of personnel, and so did the school.

This crisis went on until the end of the 16th century, when in the wake of the Counter-Reformation more and more students from South German Jesuit Colleges attended the school.

Starting from the beginning of the 1781/82 session, the Stiftsgymnasium due to Empress Maria Theresa’s education policies was referred to as gymnasium publicum, a type of school that was "partially open to the public".

Moreover, a preparatory class (praeparanda) was introduced to facilitate pupils’ transition from their small village schools to gymnasium, it persisted until 1927.