Studying the boundary layer is imperative because severe weather in this portion of the atmosphere impacts on environment and various facets of national activities and affects the socioeconomic scenario of a region. Near surface boundary layer characteristics are investigated through the vertical variation of fluxes of heat, moisture, momentum, kinetic energy and Richardson number during the pre-monsoon season (April-May) at Kharagpur (22° 30' N, 87° 20' E) and Ranchi (23° 32' N, 85° 32' E) with 50 and 32 m tower data, respectively, on thunderstorm and non-thunderstorm days. The temporal variation of fluxes within the boundary layer and the kinetic energy at different logarithmic heights are observed to vary significantly between thunderstorm and non-thunderstorm days. The heat and momentum fluxes show a maximum peak while the moisture flux shows a sudden attenuation just before the occurrence of thunderstorms. The wind field depicts to play a crucial role at the inland station Kharagpur, which is in the proximity of the Bay of Bengal, compared to the station Ranchi, situated over hilly terrain on Chotanagpur. The micrometeorological study of the boundary layer reveals a significant finding pertaining to observe the passage of thunderstorms. It is observed that the ratio of the potential temperature (θ) and equivalent potential temperature (θe) remains confined within a critical range between 0.85 and 0.90 during the passage of thunderstorms.