A thermal stabilization system stabilizes inertial measurement unit (IMU) performance by reducing or slowing operating variations over time of the internal temperature. More specifically, a thermoelectric heating/cooling device operates according to the Peltier effect, and uses thermal insulation and a mechanical assembly to thermally and mechanically couple the IMU to the thermoelectric device. The thermal stabilization system may minimize stress on the IMU and use a control system to stabilize internal IMU temperatures by judiciously and bidirectionally powering the thermoelectric heating/cooling device. The thermal stabilization system also may use compensation algorithms to reduce or counter residual IMU output errors from a variety of causes such as thermal gradients and imperfect colocation of the IMU temperature sensor with inertial sensors.