Its origins date back to the end of the 19th century, when Ljubljana Bishop Anton Bonaventura Jeglič presented the idea of creating the first fully Slovene-language upper secondary school.

[2] After the war, the premises were used as a collection center for captured Slovene Home Guard troops, most of whom were later killed.

Classes started being held again at the Episcopal Classical Secondary School (Škofijska klasična gimnazija), which is housed by the institute, on 1 September 1993.

In addition to the Episcopal Classical Secondary School, today the St. Stanislaus Institute also houses the Jeglič Dormitory for Boarding Students (Jegličev dijaški dom), the Janez Frančišek Gnidovec Student Residence (Študentski dom Janeza Frančiška Gnidovca), a music school, the Slovenian Center (Slovenski dom), the Good Shepherd Preschool (Vrtec Dobrega pastirja), and Alojzij Šuštar Elementary School (Osnovna šola Alojzija Šuštarja).

The directors of the institute after it was reopened have been Borut Košir from 1993 to 2000, Anton Jamnik from 2000 to 2006, Roman Globokar from 2006 to 2018, and Tone Česen since 2018.