[4] The university traces its origins to Fudan College, established in 1905 by Chinese Jesuit priest Ma Xiangbo.

Prior to founding Fudan, Ma had established Aurora College, where the Society of Jesus frequently opposed and intervened in student movements.

[5]: 71  In China under Chiang Kai-shek and the Kuomintang, Fudan University was tasked with providing a Western-style education to Chinese students to support the country's economic reconstruction efforts.

[5]: 81  In China under Mao Zedong, Fudan University was tasked with transmitting socialist values to further the agenda of the CCP.

[6][7] In December 2019, Fudan University changed its constitution, removing the phrase "academic independence and freedom of thought" (學術獨立和思想自由) and including a "pledge to follow the Communist party's leadership" (學校堅持中國共產黨的領導), leading to protests among the students.

[16] Fudan has five undergraduate colleges – Zhide (志德), Tengfei (腾飞), Keqing (克卿), Renzhong (任重), and Xide (希德).

The university has four campuses in Shanghai – Handan (邯郸), Fenglin (枫林), Zhangjiang (张江), and Jiangwan (江湾) – which share the same central administration.

[18] As of 2024,[update] Fudan remains the main location, but some elements of the course are also delivered at Durham and in San Francisco, USA.