This paper presents an experimental study of a new liquid cooling circuit and its control strategies. The objective is to meet the heat management requirements of a Proton Exchange Membrane Fuel Cell during startup. The cooling circuit creates an alternate flow through the stack. The cell heat generation is achieved by inserting heating pads enabling the study of the heat transfer behavior independently of the electrochemical reaction. New circuit control strategies are compared to reference strategies for no flow circulation or unidirectional flow. The alternate flow duty cycle is adjustable, and the stages where fluid is at rest in the fuel cell can be included. We show that this new cooling system can ensure a temperature rise of 26°C in 85 s. A maximum temperature difference between the bottom and top part of the cells of 1°C and 3°C along the stack is observed.