Abstract This paper depicts about the cooling system of prismatic batteries as these batteries are space efficient for electric vehicles. Although these batteries are well known for their high heat dissipation while charging and discharging the thermal management of the battery should be in such a way that these batteries need a cooling environment to reduce the heat. In this paper, a three-dimensional CFD study is presented for cell-to-cell heat generation in the battery module. The battery module is comprised of uniformly spaced three prismatic Li-ion cells. Large spacing is assumed for safer removal of cell reaction gases in modules. The cell heat generation is computed based on the thermal model. The battery module experiences a higher temperature on the upstream side as the fluid passes across each row of cells and absorb the battery heat. Throughout the discharging process, maximum battery temperature and cell temperature uniformity are found much lower than permissible range applicable for safe operation of Li-ion module. The maximum battery temperature at discrete hot location is observed up to 34 °C, 45 °C and 60 °C respectively at 900 s, 1800 s and 3600 s. The maximum rate of heat dissipation is observed from battery 2 and its value varies from 2.83 W to 17.86 W respectively at battery discharging duration of 300 s and 3600 s. The maximum cell temperature non-uniformity in a battery module is observed 0.019 °C to 0.99 °C respectively at 300 s and 3600 s. The effect of interspacing of the batteries as well as inline and staggered arrangement within the module is needed to be analyzed in detail for efficient cooling system.