The Institute for Pesticides and Environmental Protection has its early roots in the Institute for the Application of Nuclear Energy (INEP), which was founded in 1959 as the Institute for the Application of Nuclear Energy in Agriculture, Veterinary Medicine and Forestry. In 1960, it moved into seven buildings that formed its new seat and received 52 hectares of experimental fields from a previous Small Grains Experimental Station of the Faculty of Agriculture, Belgrade University in Zemun.

The decision on founding INEP as an inter-faculty scientific and educational institution was adopted by the Belgrade University Council on September 19, 1959 at the proposal of the Faculties of Agriculture, Veterinary Medicine and Forestry under the auspices of the Federal Commission for Nuclear Energy. The decision was approved by Serbia’s National Assembly under its own decision No. 160 of May 18, 1960. The decisions enabled that laboratories focusing on applications of radioisotopes that existed at various faculties of Belgrade University at the times be united under the same roof, creating a specific and unique research institution in the former state. The focus of that institution was primarily on fundamental and applied research and specialization in life sciences, biological science and biomedicine, and the application of radioactive and stable isotopes, as well as ionizing radiation in those fields of research.

At the end of 1991, the Institute for Pesticides and Environmental Protection, a constituent part of INEP, broke away and joined the Agricultural Research Institute “Serbia”, which was founded earlier that year in the aftermath of transformation of a previous agricultural research institution of the same name “Serbia”. Based on a decision by the Ministry of Science and Technologies of the Republic of Serbia No. 640-01-22/91-03 of July 31, 1991, Institute “Serbia” was registered as a research institution by the Regional Court of Commerce in Belgrade under decision FI-12511/91 of December 24, 1991. The earlier Institute for Pesticides and Environmental Protection was then newly registered as the Center for Pesticides Research and Environmental Protection, a part of the Institute “Serbia”, under another decision of the same court FI-12516/91 of December 24, 1991.

After a new Scientific Research Act was adopted in 2005 (Official Gazzete of Republic of Serbia, 110/05), all research centers of the Institute of Agricultural Research “Serbia” decided to break away and seek individual registration as research organizations. The Government of Serbia verified a decision to that effect on September 18, 2006 (Official Gazzete of Republic of Serbia 78/06), and the Center for Pesticides Research and Environmental Protection of Institute “Serbia” was as a result registered as an independent state-owned research organization named the Institute for Pesticides and Environmental Protection under a decision by the Belgrade Court of Commerce No. XII Fi 337/06 of November 1, 2006. Its current seat is at Banatska 31b in Belgrade’s municipality of Zemun, and it has been categorized as a research and development institute.