1995 On the 90th anniversary of Fudan University, President Jiang Zemin wrote an inscription for Fudan University: Facing the new century, build Fudan University into a world-class comprehensive socialist university.

On April 27th, 2000, Shanghai Medical University merged with Fudan University to form a new Fudan University. The merger of Shanghai Medical University and Fudan University has further broadened the discipline structure of Fudan University and laid a solid foundation for the development goal of building a world-class comprehensive university.

In 2005, President Hu Jintao sent a congratulatory letter, calling Fudan University "the first university independently founded by China people". The National People's Congress Standing Committee (NPCSC) Chairman Wu Bangguo attended the celebration meeting and delivered a speech. The State General Post Office issued the centennial stamps of Fudan University, which is the second time that China issued the centennial stamps of the university after the centennial celebration of Peking University. In 2006, "Fudan" was awarded a famous trademark in Shanghai; In 2007, the trademark "Fudan" (including the word "Fudan" and graphic logo) was recognized as a well-known trademark in China by the Trademark Office of the State Administration for Industry and Commerce, making Fudan the second university in China to receive this honor after Tsinghua. The University of Tokyo only accepts students who have graduated with honors from Peking University, Fudan University and Tsinghua University in China, and who have been recommended by the president of the university to study master's courses and professional degree courses at the university, and grants scholarships to the ADK China Yu Ying Fund, which is mainly used to help train the next generation of leaders in various fields in China.