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More variable renewable energy sources and energy efficiency measures create an additional flexibility gap and require a novel energy planning method for sustainable national energy systems. The firstly presented method uses only EnergyPLAN tool in order to decrease the flexibility gap in a national energy system. Generic Optimization program (GenOpt ® ) is an optimization program for the minimization of a cost function that is evaluated by an external simulation program, such as EnergyPLAN, which was used as the second method in this research. Successful strategies to decrease the flexibility gap are verified on the case of the Serbian national energy system using two methods for its structure design: (1) the iterative method, based on heuristics and manual procedure of using only EnergyPLAN, and (2) the optimization method, based on soft-linking of EnergyPLAN with GenOpt ® . The latter method, named EPOPT (EnergyPlan-genOPT), found the solution for the structure of the sustainable national energy system at the total cost of 8190 M€, while the iterative method was only able to find solutions at the cost in the range of 8251–8598 M€ by targeting only one sustainability goal. The advantages of the EPOPT method are its accuracy, user-friendliness and minimal costs, are valuable for planners. [ABSTRACT FROM AUTHOR]