The Department of Pharmaceutical Analysis was founded in the 1950s at Shanghai First Medical College. In 2000, with the merger of Shanghai Medical University and Fudan University, a new pharmaceutical analysis discipline was formed at School of Pharmacy, Fudan University. At the beginning of 2009, in response to the School's "One Body and Two Wings" development strategy, the entire discipline was relocated from the Fenglin Campus to the Zhangjiang Campus. In 1961, pharmaceutical analysis department began to recruit graduate students and in 1981 and 2012, master and Ph.D. programs were set up respectively.

After more than half a century of development, the Department of Pharmaceutical Analysis has made great progress in personnel training and scientific research. Since 2002, the research fields have been further expanded, covering three aspects including spectroscopy, electrochemistry, and chromatographic analysis.