In Szeged, the subject Pharmaceutical Chemistry was initially taught at the Institute of Chemistry, Ferencz József University of Sciences. This institute was later divided up. Professor Tibor Széki became head of one of the new departments, and lectured on both Organic Chemistry and Pharmaceutical Chemistry.

In 1938, Professor Győző Bruckner took over the Institute of Organic and Pharmaceutical Chemistry. In 1947, the Institute of Pharmaceutical Chemistry was was set up as a separate institute, headed by Professor Dénes Kőszeg, who had lectured on this subject since 1935. At that time, the drug compounds included mainly inorganic molecules, and the education and research therefore concentrated on the preparation and analysis of these compounds. Professor Elemér Vinkler, who had earlier lectured on organic drug compounds, headed the Institute between 1963 and 1979. Professor Vinkler was fully at home with organic chemistry and dealt with organic sulfur compounds in his research work. Hence, the research profile turned to synthetic preparative organic chemistry from 1964. In this way, the research and education were harmonized with the international trends: at that time, it was obvious that mainly organic compounds would be applied in therapy.

Between 1979 and 1998, when Professor Gábor Bernáth was head, the research and education profile moved further towards the synthetic organic chemistry of saturated heterocyclic compounds, and an up-to-date stereochemical approach was emphasized in the education too.

Since 1998, the present head, Professor Ferenc Fülöp has been leading studies on the saturated heterocycles, enzymatic resolution and the synthesis of asymmetric molecules. The cumulative impact factor of the 20-25 The number of scientific publications published annually rose to over 54 in 1998. This fact and the previously achieved numerous D.Sc., C.Sc. and Ph.D. degrees all prove that, during the past 35 years, the Institute of Pharmaceutical Chemistry has been the center of research and education in Pharmaceutical and Organic Chemistry in Southern Hungary.

In 2017, Professor Loránd Kiss became head of the Institute. The Professor extended the preparation of alicyclic synthetic bulilding blocks with organic fluorchemical methods.

From the summer of 2021, the institute operates under the direction of István Szatmári, associate professor, whose aim is to detect new directions of heterocycle chemical research with high traditions at the Institute. The institute's five synthetic organic chemical laboratories equipped with instruments, which are needed to establish the structures of new compounds (NMR, GC-LC-HRMS, IR and spe UV spectrometers, polarimeter, GC and HPLC instruments).