The Institute of geography was established as the Department of Geography in 1998 within the structure of the Faculty of Science of the Pavol Jozef Šafárik University in Košice. Assoc. Prof. Zdenko Hochmuth was the founder and the first Head of Institute. During the early years, the Department of Geography oriented towards the education of teachers (MSc.) of Geography in combination with other subject (Mathematics, Physics, Biology, Chemistry, and Computer Science). Research was focused on Physical Geography (Geomorphology, Karsology, Hydrology, Geology of the Quarternary, Soil science) which reflected the scientific background of the academic staff working at the Institute (doc. RNDr. Zdenko Hochmuth, CSc., prof. RNDr. Ján Košťálik, DrSc., RNDr. Dušan Barabas, CSc.).

The Department of Geography transformed into the Institute of Geography in 2004. The structure of the academic staff had been significantly improved by researchers in Human Geography and Regional Geography. The portfolio of study programmes had been enlarged by the research oriented Geography programme both on undergraduate level (BSc.) and postgraduate taught level (MSc.). Progress of the Institute was stabilized by employing Professor Peter Spišiak. Afterwards, the research activities gradually expanded into the specific fields of human geography and regional geography (study of urban structure and transformation, rural and suburban structures, and population migration).

Further stimulus of development was in achieving success in national and international grant schemes supported by the European Union. These resources enabled procuring modern research and educational infrastructure and also establishing specialised laboratories. The arrival of Professor Jaroslav Hofierka in 2012 further consolidated the Institute educational and research profile. Later in 2103, he was designated the Head of Institute. The Institute was reorganized and three research groups were officially established: Physical Geography, Human Geography and Regional Geography, and Geographic Information Science. This step reflects the natural structure of the staff and research orientation of its members.