EnergyPLAN is an energy system analysis tool created for the study and research in the design of future sustainable energy solutions with a special focus on energy systems with high shares of renewable energy sources. The tool has been under development since 1999 and has formed the basis for a substantial number of PhD theses and several hundreds of research papers. EnergyPLAN is designed to exploit the synergies enabled from including the whole energy system, as expressed in the smart energy system concept. Thus, with EnergyPLAN, the user can take a holistic approach focusing on the analysis of the cross-sectoral interaction. Traditionally disparate demand sectors, such as buildings, industry and transport, are linked with supply technologies through electricity, gas, district heating and cooling grids. In this way, EnergyPLAN enables the analysis of the conversion of renewable electricity into other energy carriers, such as heat, hydrogen, green gases and electrofuels, as well as the implementation of energy efficiency improvements and energy conservation. This article describes the overall structure of EnergyPLAN and the essential algorithms and computational structure.