The institution was originally established in Beijing in 1925 by the Benedictines of St. Vincent Archabbey in Latrobe, Pennsylvania at request of the Holy See. Fu Jen, then known commonly as the Catholic University of Peking, was itself a successor to the Fu Jen Academy (輔仁社), which was created through the efforts of Catholic scholars Ma Xiangbo and Ying Lianzhi. The university's first president (1925–1927) was the American missionary George Barry O'Toole, OSB. He was succeeded by Chen Yuan (陳垣), a Chinese Protestant, who remained university president until the school's forced closure by the Chinese government in 1952.
The laurel wreath symbolizes honor and peace while the twelve stars signify the Virgin Mary. The cross represents the Christian faith. The two colors on the shield suggest Christ's dual nature as the rounded shape of the shield recalls the sacred heart. The Latin words on the banner beneath the emblem express the four ideals of the university while the three folds of the banner suggest the Trinity.
Fu Jen Academia Catholica was inaugurated on August 1, 2008 to enable interdisciplinary pursuits in Catholic studies. The Academia consists of five Fu Jen academic institutes or centers: the Institute of Scholastic Philosophy, Institutem Historiae Ecclesiae, Center for the Study of Science and Religion, Monumenta Serica Sinological Research Center, and John Paul II Institute for Research into Dialogue for Peace.
Fu Jen established Taiwan's first graduate-level program in conference interpreting. The Graduate Institute of Translation and Interpreting Studies (GITIS) (翻譯學研究所) is the only MA-granting program in a private university conferring degrees and training in translation and interpretation in Chinese<>English and Chinese<>Japanese combinations (Chinese<>French having been discontinued.) Small class sizes and individualized attention from faculty keep the program popular among applicants and its graduates remain highly competitive on both the Taiwanese and international markets.
Fu Jen has annexed a Mandarin Language Center (語言中心), established in 1964 to address the need for the foreign missionaries to learn Chinese. In 1969, with the approval of the Ministry of Education the center was renamed as “Language Center” (LC), which teaches non-degree Mandarin Chinese courses, also Taiwanese and every semester opens different cultural classes as Chinese Poetry, Calligraphy and Taijiquan. The LC has hundred of students every semester from different parts of the world.