An active thermal management system for a fuel cell stack controls the distribution of coolant flow for each unit cell of the fuel cell stack based on the temperature distribution measured at unit cells of the fuel cell stack. A coolant distribution means is capable of controlling the distribution of coolant flow for different sets of unit cells. The coolant distribution means is disposed in a coolant inlet manifold, and controls the coolant flow based on the temperature distribution measured at different unit cells of the fuel cell stack so as to reduce temperature variation in the unit cells, thus improving the performance and durability of the fuel cell stack.