The sustainable use and management of groundwater resources is now a great challenge for many countries of the world. Recently groundwater modelling has been an effective way to address this challenge. There are a number of modelling software exist to simulate groundwater flow. Among them two modelling software - MIKE SHE and MODFLOW were used to develop two individual groundwater models and a comparison of these model’s output is presented in this paper. The main difference between these two modelling software is that MIKE SHE includes unsaturated zone whereas MODFLOW deals with saturated zone only. Using existing hydro-geological and meteorological data, two models were developed and calibrated for the high Barind area of Bangladesh in layers of five distinct vertical deposits, namely Clay Top, Upper Aquifer, Clay Middle, Lower Aquifer and Clay Bottom). The difference of groundwater flow hydrographs from two models and the probable reasons behind the difference are discussed. The important calibration parameters are being depicted in this paper.