Long-term energy scenarios (LTES) have been serving as an important planning tool by a wide range of institutions. This article focuses on how LTES have been used (and also devised in some cases) in the government sector, and specifically how the new challenges and opportunities brought by the aspiration for the clean energy transition change the way that governments use LTES. The information tends to remain tacit, and a gap exists in understanding the way to enhance LTES use and development at the government level. To address this gap, we draw on the experience from national institutions that are leading the improvement in official energy scenario planning to articulate a set of overarching best practices to (i) strengthen LTES development, (ii) effectively use LTES for strategic energy planning and (iii) enhance institutional capacity for LTES-based energy planning, all in the context of new challenges associated with the clean energy transition. We present implementation experience collected through the International Renewable Agency’s LTES Network activities to exemplify these best practices. We highlight that in the context of the broad and complex challenges of a clean energy transition driven by ambitious climate targets, the LTES-based energy planning methodologies need to evolve, reflecting the changing landscapes, and that more effective and extensive use of LTES in government needs to be further encouraged.