GIS Cell is an interdisciplinary department of the institute which was established in the year 2006. It offers M.Tech. and PhD programme in Geoinformatics. Additionally, GIS Cell conducts research in all major disciplines of Geospatial technology namely Global Navigation Satellite System (GNSS), Geographic Information System (GIS), Satellite Image Processing, Advance SAR Interferometry and LiDAR Technology, Mobile Mapping. The evolution of Geoinformatics has been marked by significant advancements, beginning with traditional cartography and land surveying. Since the last two decades, Geoinformatics saw broader applications in urban planning, environmental monitoring, and disaster management, driven by open-source GIS tools and the integration of big data analytics. Recent years have witnessed the transformation of Geoinformatics through cloud computing, artificial intelligence, machine learning, and the Internet of Things, enabling real-time data collection, sophisticated spatial analysis, and enhanced 3D visualization. Today, Geoinformatics is essential in various sectors, including sustainable development and geospatial intelligence, with ongoing innovations promising even broader applications and advancements in the future.

MNNIT Allahabad has taken an early initiative in this field by establishing GIS Cell, and is among few premier technical Institutes of India to offer M.Tech. in Geinformatics (erstwhile GIS and Remote Sensing) from academic session 2006-07. GIS Cell has faculty of its own as well as faculty members from various other departments of institutes. The Cell has been granted the status equivalent of a Department by the Institute for running postgraduate programmes offer course at graduate level.  The Cell is equipped with state-of-the-art laboratory facilities and a well-defined course structure and undertakes research in wide-range of research interests such as in Satellite Geodesy (primarily InSAR and GNSS), Remote Sensing, Laser Scanning, GIS, and Sensor Integration. GIS Cell also offers Institute fellowship for carrying research work leading to the award of Ph.D. degree in the field of Geoinformatics (Core and Applications).