A fuel separation apparatus comprises a stock fuel storage tank storing stock fuel, a separator provided with a separation film separating the stock fuel into high octane value fuel with an octane value higher than the stock fuel and a low octane value fuel with an octane value lower than the stock fuel, and a high octane value fuel storage tank storing the high octane value fuel separated by the separator. When the temperature of the separation film is lower than the high octane value fuel separation temperature, the high octane value fuel stored in the high octane value fuel storage tank is supplied to the separator. Due to this, vaporization of fuel is suppressed and the fuel can be quickly raised in temperature. Due to this, a vehicle mounted fuel separation apparatus able to quickly raise the temperature of the fuel supplied to the separation film so as to quickly raise the temperature of the separation film at the time of engine cold start can be provided.