An algorithm for determining a polarization curve of a fuel cell stack. When the fuel cell stack is running and certain data validity criteria have been met, the algorithm goes into a data collection mode where it collects stack data, such as stack current density, average cell voltage and minimum cell voltage. When the stack is shut down, the algorithm uses a cell voltage model to solve a least squares problem to estimate predetermined parameters that define the polarization curve. If the estimated parameters satisfy certain termination criteria, then the estimated parameters are stored to be used by a system controller to calculate the polarization curve of the stack.