In an effort to improve services at the Orphanage he manages, Monseigneur (Mgr) Lijnen, Parish Priest of Gedangan Semarang in the late 1860s took the initiative to bring in Sisters from the Congregation of the Sisters of Saint Francis in Heythuysen Netherlands to carry out missions in the Dutch East Indies (Indonesia). After going through a long journey across the ocean for almost 6 months, on February 5, 1870 the ship Jacoba Cornelia carrying 11 Sisters of the Order of St. Francis (OSF) docked at the port of Semarang.
Although at first the arrival of the Sisters worked at the Orphanage, over time and the development of needs, they also developed activities in the fields of education, health and social affairs. Its service area coverage has also expanded not only to Semarang but also to other cities including Yogyakarta.
On March 19, 1902, four OSF Sisters came from Semarang to Yogyakarta. They are Sr. Fransisca Versteegh, Sr. Eulabie Sloesen, Sr. Jacobine Wartel and Sr. Anthony Lunders. On April 1, 1902 the OSF Sisters began to open a school for girls called Frobel School. Then, on July 1, 1902, the OSF Sisters began to open an elementary school, which was named Leerschool. The number of students at first was only 50 people. However, from year to year the number of students increased so that they needed more extensive facilities. On April 19, 1904, a groundbreaking ceremony was held for the construction of the monastery and school complex. The blessing of the new building complex, which was named Maria School (School of Santa Maria), took place on December 8, 1904. On June 28, 1920, the Intemarata Elementary School was opened, which was the forerunner of SD Marsudirini.
A government regulation issued in 1952 stipulated that schools should be managed by a single foundation. Therefore the schools founded by the OSF Sisters working in Yogyakarta are under the auspices of the Kanisius Foundation. However, with various considerations, in 1954 the Marsudirini Foundation was formed which was tasked with managing and fostering the schools founded by the OSF Suters. The name Marsudirini comes from a combination of the words Mar, Su, Di, Ri, and Ni. Mar stands for Maria, Su stands for Suci, Di stands for Dyah, Ri stands for Rinumpaka, and Ni stands for Niskala. So, if these combined words become a series of words, namely Marsudirini, it has the meaning of the Virgin Mary Decorated with Purity.