Polymer Electrolyte Membrane (PEM) fuel cells are clean electrical power generators for applications normally up to 100 kW power requirements. It has the advantage of fast start-up due to its low operating temperatures of 60oC to 100oC. However, the low temperature requirement has to be addressed with an efficient thermal management system. For an air-cooled PEM fuel cell, cooling channels with a straight rectangular configuration are widely applied. This work establishes a computational methodology for the analysis of coolant flow mechanics related to the channel geometry for a specific bipolar plate size. The velocity and thermal gradient, average velocity rise factor (AVRF) and total cooling rates were determined from Computational Fluid Dynamics simulation based on initial coolant Reynolds number of approximately 250 to 750 with a steady heat flow of 82W. All geometries showed nearly 100% cooling capability respective to the heat load, but differ in the aspects of average plate temperature achieved, its temperature profile as well as existing gradient. From the analytical perspective of thermo fluids engineering, the selection criteria of suitable micro cooling channel configurations, depending on operating priority, was established.