The development and integration of an improved cooling system for the fuel cell system has been implemented on the MAHEPA Hy4 prototype aircraft. Therefore an alternative cooling with a new integration concept for the radiator was developed and implemented in CAD models. For an optimal cooling result extensive work was done on the aerodynamic shape and the air ducting via CFD calculations. These calculations led to modifications of the full thermal conditioning system with high performance improvements regarding pressure drop, cooling area and at least cooling power. Finally the cooling system has been integrated onto the MAHEPA Hy4 central wing.