The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally validated. It offers a good balance between accuracy and execution speed. The modular architecture allows for addition of new features, and it has a user-friendly graphical interface. An automatic calibration method is proposed to match the model to the studied fuel cell. The software provides information on the internal states of the system in response to any current density and can produce polarization and EIS curves. AlphaPEM facilitates the use of a model in embedded conditions, allowing real-time modification of the fuel cell’s operating conditions.