The Department was established in 1942 as Department of Pharmacognosy and Galenic Pharmacy following the setting up of the Section of Pharmacy at the Faculty of Natural Science and Mathematics at the University of Sofia. Throughout 1942 the main subject was botany at first read by Prof. N. Arnaudov then by Academician D. Yordanov. In 1943/44 a course in pharmacognosy was introduced read by A. Boichinov, Ph.D. In 1947 the Department of Pharmacognosy was established as a separate unit. Prof. A. Boichinov (1900 – 1967) was one of the founders and the first head of the department. In 1958 botany came under the responsibilities of the Department of Pharmacognosy and the department acquired its present structure. In 1968 the Laboratory of Control and Standardization of Drugs was affiliated to the department. In the year 1990 the Laboratory of Pharmaceutical Biotechnology was established by Prof. Dr. Ionkova as a part of Department of Pharmacognosy.
Heads of the Department since its establishment: Prof. A. Boichinov, Prof. H. Ahtardjiev, Prof. S. Valev, Prof. I. Assenov, and Prof. Dr. St. Nikolov since 1999.