In proton exchange membrane fuel cells (PEMFCs), the avoidance and detection of failures such as flooding and dry-out are crucial. Non-destructive measurement approaches using magnetic sensors have been developed for this purpose. To reduce the number of sensors required to be installed in a PEMFC system for evaluation, we propose a control method for PEMFCs using the magnetic flux density as an index. The proposed method determines the failure conditions by calculating a simple current mapping with a reduced number of sensors. The results of four-point magnetic flux densities under failure conditions and stable control using two-point measurement indices are presented.