System and methods for setting pressure limits for an air supply of a fuel cell (“FC”) system are presented. Certain embodiments disclosed herein may allow a FC system to calculate a minimum and a maximum FC stack cathode inlet pressure based on different operating conditions while ensuring that the FC stack receives a desired air flow. Further embodiments disclosed herein may allow a FC system to maintain a cathode inlet air pressure within a range that protects an associated compressor from entering surge and/or overheating conditions.