The school has China Language and Literature Department, Philosophy Department, History Department, Heritage and Museum Department, Foreign Language and Literature Department, Law School, School of International Relations and Public Affairs, School of Journalism, School of Economics, School of Management, School of Social Development and Public Policy, School of Mathematical Sciences, Department of Physics, Department of Chemistry, Department of Polymer Science, Department of Environmental Science and Engineering, School of Information Science and Engineering, School of Software, etc. There are 28 directly affiliated departments, including Department of Mechanics and Engineering Science, School of Life Sciences, Shanghai Medical College, School of Public Health, School of Pharmacy, School of Nursing, School of International Cultural Exchange and Department of Art and Design.

Among the graduate students who graduated from Fudan University, 14 were awarded the title of "Doctor and Master Degree Winner with Outstanding Contributions in China", among which 22 won the prize in the four national top 100 doctoral dissertations. Fudan University graduate students are widely appreciated and accepted by employers for their profound knowledge literacy, outstanding practical ability and positive innovative spirit.