Power Semiconductors undergo thermal stress during operation, which is caused by thermal cycling. This refers to heating up and cooling down of the junction temperature and leads to aging and finally failures. Active thermal control can reduce the thermal stress of power semiconductors by regulating the power losses. Most algorithms proposed so far are only applicable to hard switching power converters and implement a regulation of the switching frequency, which is not applicable for the isolated DC/DC converters. This work proposes to regulate the duty cycle of the DC/DC converter to control the semiconductor losses, aiming at influencing the consequent thermal stress. The proposed algorithm is analyzed analytically and a thermal controller is designed, which is capable of reducing thermal cycles during operation without prior knowledge about the mission profile. The capability and the limitations of the proposed algorithm are demonstrated with simulations and the effectiveness is validated on a laboratory prototype with junction temperature measurement.