Abstract During the start-up or operation of pool type lead cooled fast reactor, it is probable that loss of flow transient appears from forced circulation or mass flow rate less than that during forced circulation, due to any flow blockage, station blackout or pump malfunction. In this type of scenario temperature distribution and movement of thermal stratification layer will be different from that during loss of flow transient from forced circulation. Computational fluid dynamics (CFD) transient analysis of three-dimensional model of CLEAR-S was performed in this research with the use of commercial code FLUENT to analyze the influence of initial coolant mass flow rate on flow and coolant temperature profile in different constituents of engineering validation facility (CLEAR-S) during loss of flow transient. Firstly, steady state was simulated at mass flow rate equal to 100%, 50% and 25% of the rated mass flow rate respectively. Than loss of flow transient was simulated after started from the steady state of 100%, 50% and 25% of the rated mass flow rate as t = 0sec respectively to understand the movement and temperature distribution of thermal stratification within the pools of CLEAR-S. Results showed that after loss of flow transient from 100%, 50% and 25% mass flow rate, LBE in the hot pool was distributed into five to six layers of different temperatures and temperature of LBE on both sides of stratification layer increased with the decrease of initial mass flow rate. As time progressed hot pool stratification layer proceeded upward and width of top most layer of LBE with high temperature reduced which ultimately vanished after giving birth to a new layer at hot pool bottom. Stratification initiated from DHR outlet in the cold pool after loss of flow transient from 100% mass flow rate. Thermal stratification was observed to be started at heat exchanger (HX) outlet during loss of flow transient initiated form 50% and 25% of mass flow rate. Temperature of LBE on both sides of stratification layer increased with the decrease of initial cold pool mass flow rate of CLEAR-S. With the proceeding of time Stratification layer raised upward and top most layer vanished.