The aim of the paper is to propose a methodology for evaluating the energy sustainability of a city based on the characterization of the energy end-use, energy systems and flows, as well as other intrinsically related concepts, such as the quality of air and the energy efficiency in transport and buildings. As a result, an Urban Energy Sustainability Index (UESI) has been proposed to measure the energy sustainability of the cities. Several indicators have been proposed to be used to build the index. These indicators have been grouped into three types depending on their influence on energy urban sustainability: basic, instrumental and complementary. For each indicator, an analysis has been done and as a result an expression for estimating it has been proposed. The value of the index is obtained from the combination of these indicators using the weighted average method. The proposed index can be used as an operational tool to improve the sustainability of cities. It also aims to have an international application as it is related to the global sustainability objectives defined by internationally recognized organizations. The proposed methodology has been used for two different Spanish cities, Barcelona and Malaga. The results show that it covers most of the issues related to the use of energy and sustainability in the cities and that it can also be applied to others cities.