To increase the reliability of aerospace electronics and reduce their overall power consumption, we investigated the possibility of incorporating active thermoelectric cooling (TEC) solutions. The harsh avionic environment demands sophisticated active control schemes that enable the achievement of high coefficient of performance. The positive effect of active PWM control has been validated both in simulation and on a working laboratory prototype that allowed us to clarify the pros and cons of the incorporation of TEC techniques in avionics applications. This paper has been performed under the framework of CLEAN SKY-THERMICOOL project.