This paper describes the thermal design and analysis of the Electronic Unit (EU) of a Microgravity Vibration Isolation System (MVIS) that will ensure the active isolation of the European Space Agency's Fluid Science Laboratory (FSL) payload from vibration induced by the International Space Station (ISS) structure. The FSL is equipped with optical and electronic devices that are very sensitive to vibration, thermal distortion, temperature change and ElectroMagnetic Interference (EMI). The MVIS has to provide a vibration attenuation of -40dB within the range of 0.1-100Hz without inducing thermal or electromagnetic interferences.The sensitive FSL instruments are mounted in a floating structure called the Facility Core Element (FCE), whereas the rest of the FSL electronics, mechanics and cooling systems are fixed to the International Standard Payload Rack (ISPR). In order to minimize the FCE accelerations, the MVIS is composed of accelerometers, position sensors and magnets (attached to the FCE) that interact with coils controlled by the EU mounted on the ISPR.The 130W dissipation of the EU is rejected through the ISPR Avionic Air Loop, nominally providing an airflow rate of 350 L/minute at 25°C. A hundred fins were integrated to the EU box to ensure proper cooling of the sensitive electronics while avoiding EMI through air inlets and outlet. The thermal planes of the boards were electrically insulated from EU box, adding a difficulty to the design.The present paper summarises the thermal design of the EU with respect to the FSL and MVIS performance and safety/durability requirements. It also presents and compares the thermal analysis of the EU performed with I-DEAS TMG code and a coupled thermal and Computation Fluid Dynamics (CFD) analysis performed with the I-DEAS ESC code.