Among the three departments within the Lyceum, the Zoological Department was established in 1853. Zoology and several other “natural” subjects were taught at that time by Dr. Josif Pančić. Later, from the Zoological Department at the Department of Natural Sciences and Mathematics of the Faculty of Philosophy, and from 1889 within the Department of Natural Sciences and Chemistry of the Faculty of Philosophy, in addition to lectures, student internships were introduced for the first time in the teaching. These were the first institutions that we consider the forerunners of today's Institute of Zoology.

Dr. Živojin Đorđević organized teaching and science in the style of the most famous European universities of that time. In addition to general zoology, cytology, histology and embryology, he introduced for the first time the study of applied sciences (parasitology, epidemiology, fisheries, zootechnics). He also introduced practical exercises and knowledge of microscopic methods, techniques and procedures, within the first biological research and scientific laboratory.

At the beginning of the 20th century, the Zoological and Physiological Institute was formed, belonging to the newly formed Belgrade University, in 1905. The First World War interrupted all activities, a large number of students and professors were mobilized, and the book fund of the Zoological Institute, as well as professional collections, were partially destroyed.

Between the two wars, the Institute was modernized and new areas of research (hydrobiology, limnology), new disciplines (genetics, ecology), as well as new forms of teaching were introduced. Teaching and scientific activities were organized within the Department of Zoology in the building at Studentski trg 3.

The first director of the Zoological Institute after World War II was Dr. Sinisa Stankovic. Since 1947, the Zoological Institute has operated within the Biology Department of the Faculty of Natural Sciences and Mathematics of the University of Belgrade. In 1948, it returned to the reconstructed building at Studentski trg 3, in Belgrade, where it is still located today. Courses were organized in the subjects Comparative Morphology and Systematics of Invertebrates, Comparative Morphology and Systematics of Chordates, Organic Evolution, Ecology and Zoogeography, which, with the modernization of the content and certain changes in the organization of the material, have been held to this day. Postgraduate studies, lasting two years, were introduced in 1956. Graduated biologists further advanced their skills in the fields of ecology, zoopsychology, entomology, beekeeping and the dynamics of animal development.

Based on the first faunistic, later protozoological and entomological research of Dr. Josif Pančić and Dr. Živojin Đorđević and their associates, more serious scientific research work at the Zoological Institute began in the first decades after World War II. Under the leadership of Dr. Siniša Stanković, the then Institute was a vibrant place of scientific activity. The study of relict and endemic fauna, problems of speciation, population genetic research, zoosociological studies, embryonic enzyme mechanisms, are only part of the scientific activities that teachers and assistants were engaged in during this period.

In the early 1970s, a new era began for the former Zoological Institute, which changed its name to the Institute of Zoology. The Institute represented one of the three functional units of the Department of Biological Sciences within the Faculty of Natural Sciences. There was a differentiation of scientific disciplines and their integration according to their relatedness, and during that period, four departments operated at the Institute: the Department of Comparative Morphology and Systematics of Animals (today the Department of Morphology, Systematics and Phylogeny of Animals); the Department of Ecology and Geography of Animals; the Department of Dynamics of Animal Development; and the Department of Evolution (today the Department of Genetics and Evolution). In addition to the aforementioned, two more departments were later established at the Institute: the Department of Cell and Tissue Biology (2008) and the Department of Invertebrate Zoology and Entomology (2010).

The Institute of Zoology has been part of the Faculty of Biology - University of Belgrade since 1990. Departments have become the basic units for organizing teaching and scientific activities, and a large number of teachers and assistants have spent time in famous scientific centers around the world for advanced training.

Today, the Institute of Zoology consists of 90 members of staff, including 16 full and 10 associate professors, 16 associate professors, four assistant professors, one scientific advisor, four senior scientific associates, 13 scientific associates, eight research associates, six research interns, as well as 12 non-teaching staff. One visiting professor is engaged in teaching doctoral studies. Since 2021, Prof. Dr. Željko Tomanović has been a corresponding member of the Serbian Academy of Sciences and Arts.

Scientific work at the Institute is carried out in the following scientific areas: Morphology, systematics and phylogeny of animals; Cell and tissue biology; Animal developmental biology; Genetics and evolution; Ecology, biogeography and environmental protection. In the period 2012-2022, teachers and associates of the Institute of Zoology published 2.758 papers from the SCI list. The Institute of Zoology houses the following centers: Center for Bee Biology, Center for Biospeleology, Center for Electron Microscopy, Center for Genotyping of Fisheries Resources and Center for Biodiversity Information.

After the renovation of the so-called "attic space" in 2001, the departments received equipped laboratories for scientific research and a cold chamber and an incubator for growing insects. The institute's lecture halls are equipped with modern technology and school microscopes, the library with new computers and also serves as a computer lecture hall. Since 2012, the following have been built at the Institute: a PCR laboratory, intended for master's and doctoral students, a laboratory of the Center for Electron Microscopy and a laboratory of the Center for Genotyping of Fisheries Resources.

The library of the Institute of Zoology possesses a large number of valuable and very rare works. The oldest book dates from 1790 ("Betrahtung uber die Natur"), and the oldest book in the Serbian language is "Analytical and systematic review of animals in the Kingdom of Serbia, Part II - Invertebrates" from 1883. There is a constant trend of increasing the number of bibliographic units, the fund is renewed from the Faculty's funds intended for the improvement of teaching, from scientific projects, donations and constant exchange with other institutions. Currently, the library of the Institute of Zoology has 6.850 books, or 10.683 copies of books, 435 scientific journals, 12.203 separate items (500 separate items have been translated into electronic form), 1.290 diploma theses and 210 master's theses. The library is part of the SOV!55 system (http://www.vbs.rs) and currently has 2.982 records in the electronic database.