He baptized the first Javanese at Sendangsono, founded a school for teachers in Muntilan, and fought for the education of Javanese people during the Dutch colonial rule.
He was renowned because of his ability to synchronize Roman Catholic teachings with that of Kejawen so that it could be accepted by the Javanese societies. Today in Eastern and Central java, Catholicism is a religion practised by quite a number of Javanese and people from the Chinese ethnic group.
Pope John Paul II, when giving a speech in Yogyakarta in 10 October 1989, said that he stood on that day at the center of the Island of Java to commemorate those who had laid the foundations of the Catholic people, Father van Lith SJ and two of his disciples, Mgr Soegijapranata and mister IJ Kasimo.
Van Lith arrived in Semarang in 1896 to study the culture and customs of Java. He was placed in Muntilan in 1897. He stayed in Desa Semampir at the banks of River Lamat. In 14 December 1904, van Lith baptized 171 villagers from the region of Kalibawang in Sendangsono, Kulon Progo. This event is viewed as the birth of the Church among the Javanese when the 171 people become the first Javanese to embrace Catholicism. The location of the baptism is now the pilgrimage center Sendangsono.
In 1911 the seminary was officially founded, the first in Indonesia, built in part because some of the school's alumni wanted to become priests. One of them was Mgr A. Soegijapranata SJ (1896-1963), who would become the Archbishop of Semarang, the first Indonesian native bishop.
The small church and school at Semampir would then develop into a complex of buildings, which was named Kolese Franciscus Xaverius in 1911. In 1948, the school complex was burned.
This education beginning in Muntilan would create Indonesian Catholic politicians, such as Kasimo, Frans Seda, amongst others.
In Klaten, van Lith tried to establish HIS. Initially the effort did not receive the permission of the Assistant Resident, because in Klaten there was already a Protestant HIS. Because of the refusal, Father van Lith proposed directly to the Resident of Surakarta (Solo). His proposal was accepted, and in 1920 HIS Kanisius Klaten was established and education activities started at houses.
Van Lith fought for the education of the native Javanese. He sent students to Dutch universities and urged the Society of Jesus to build colleges.
He was also recommeded as member of the "Volksraad" (People's Council) by the Sarekat Islam Party, led by van Lith's close friend, K.H. Agus Salim. However, he was never elected to the People's Council.
During his time as member of both the Education Council and the Commission for Hearing of the Statehood of the Dutch Indies, Father van Lith fought for the causes of the native Indonesians, something which the Dutch government did not like. In 1920 van Lith returned to the Netherlands to tend for his faltering health. When he tried to return to Indonesia, he faced opposition from the Dutch government.