Abstract In the current fuel cell modeling literature there is a gap between “physics-oriented” cell-level models and “application-oriented” system-level models. This paper presents a computational approach to close this gap by directly coupling cell-level and system-level simulation software. It allows to integrate a detailed description of electrochemistry and 2D transport into a system model within SIMULINK, allowing a direct feedback between system requirements and cell processes. By decoupling time scales between cell and system, the computational speed can be significantly enhanced. The method is applicable to both, polymer electrolyte fuel cells (PEFC) and solid oxide fuel cells (SOFC). Here, we show application in the context of PEFCs. Local membrane water management and electrochemical performance is made accessible on the system-level, where it can be used for visualization and control purposes.