Safeguarding affordable and energy-efficient medical services has emerged as a crucial necessity to sustain national healthcare systems, especially in view of the current pandemic. While a set of national standards and guidelines aim to set minimum energy requirements for the building facilities, more insight into the healthcare sector’s energy consumption in Cyprus is deemed necessary, since it is the 4th most energy-demanding sector per square meter in this country. This is the first extended research on energy consumption in healthcare facilities across the different climatic zones of Cyprus and the types of fuel favoured in each zone, which marks the novelty of this work. The findings of the study highlight that the coastal and inland climatic zones are the most energy-challenging regions, with more than 60% of the final energy needs covered by electricity. On the contrary, in the mountainous region, approximately 80% of the final energy needs are covered by oil and attributed mainly to heating purposes. The average national primary energy consumption of healthcare facilities was found to be 497 kWh/m2 in air-conditioned spaces. Therefore, this study highlights that the mean primary energy consumption per building surface is approximately 4 times higher than the national threshold for nZEBs; compelling critical consideration of intervention for their energy enhancement. Moreover, healthcare facilities in mountainous regions in Cyprus are heavily reliant on conventional fuel; an unreliable and highly polluting energy option. The work demonstrates the prominent challenge and high potential for energy retrofit of the examined facilities and their upgrading to nZEB-Hospitals, towards the endeavour to a climate-neutral energy transition.