This study aims to determine the optimal fuel choice from a well-to-wake energy perspective by means of a comparative energy analysis of real-world fleet operations using green liquid hydrogen and synthetic sustainable aviation fuel. A calibrated Boeing 737-800NG model was developed using the SUAVE aircraft design tool, and a validated surrogate propulsion model was developed within NPSS and integrated into SUAVE. Three hydrogen aircraft, with various tank technology levels and an extended fuselage, were sized for the baseline design mission, maintaining fixed passenger capacity and design range. The in-flight energy performance of the hydrogen and sustainable aviation fuel aircraft were compared for the 29 real-world missions, in which the hydrogen aircraft yielded worse in-flight performance for all flights. However, when analysing the well-to-wake energy consumption and renewable electricity requirements, substantial energy savings could be obtained for the hydrogen aircraft, which may be desirable to reduce the significant strain placed on renewable electricity resources. Furthermore, it was found that a tank gravimetric efficiency of 50% was sufficient for superior performance of hydrogen aircraft against all SAF scenarios, further highlighting the potential of green hydrogen to minimise the energy demand of short-haul aviation over synthetic SAF in the context of decarbonisation.