Pavlov was invited to the Institute of Experimental Medicine in St. Petersburg to organize and direct the Department of Physiology.

Over a 45-year period, under his direction, the institute became one of the most important centers of physiological research in the world. Pavlov continued to direct the Department of Physiology at the institute, while taking up the chair of physiology at the Medical Military Academy in 1895. Pavlov would head the physiology department at the academy