Urban Building Energy Modelling (UBEM) represents a comprehensive approach to investigate the intricate interplay of the various factors impacting energy use of groups of buildings, offering invaluable insights for urban planners, architects, building engineers, and policymakers. Nonetheless, available UBEM tools are still “research tools” and lack a unified standard addressing input, output, nomenclature, and calculation approaches. In this context, this study aims to conduct a comprehensive comparative analysis of two of the most used UBEM tools: Integrated Computational Design (iCD), the commercial tool provided by the Integrated Environmental Solutions (IES) company, and Urban Modelling Interface (umi), developed by the Massachusetts Institute of Technology (MIT). The comparative analysis includes each step of the UBEM workflow: the creation of the model, the assignment of input data, energy simulation, and visualisation and exportation of results. The tools are tested through the simulation of a case study to provide insights on the rationale and informed use of the tools, highlighting the risks associated with use by modellers with different levels of expertise. Moreover, this study provides tool developers and the scientific community with suggestions for major areas of improvement and standardisation in the field of UBEM, since substantial differences are still reported with respect to output, input, nomenclature, and calculation approaches.