In this paper, we present, to the best of our knowledge, the first low-loss vacuum-compatible thermally controlled Faraday isolator able to retain a good isolation factor under high-vacuum working conditions. The throughput that can be obtained with the developed device is as high as 99%, retaining an isolation factor higher than 40 dB. That very high isolation ratio can be kept over long time periods independently from external temperature conditions with a few Celsius degrees of variation due to thermal active control. The mechanical and optical configuration is detailed, and the performances achieved with this device are presented.