This paper presents the procedure for conducting cost-optimal energy performance calculations for a new nearly zero energy hotel building in Croatia in the context of Energy Performance of Buildings Directive 2010/31/EU. For this purpose, dynamic simulation models of building and its technical systems were developed in IDA ICE simulating tool and coupled with GenOpt optimization software.Annual energy performance of the building is assessed by running hourly simulations. Energy, equipment and installation works costs were obtained by the open market analysis. After that, the global cost function was derived, and optimization performed to minimize the costs. The results show that the preferred heat source at the cost-optimal level of the building energy performance is air-to-water heat pump coupled with gas condensing boiler. Furthermore, an analysis of thermal comfort is provided to demonstrate the use of the proposed approach in preventing system oversizing, efficiency decrease and thermal comfort deterioration. At the end, energy performance calculations obtained by IDA ICE were compared to those obtained by the widely used EN 13790 and EN 15316 series of standards used for determining energy performance of buildings for legal purposes. Based on this, the recorded discrepancies in results are analysed and applicability of mentioned standards calculations on low-energy buildings is discussed.