Passive energy systems hold the potential to achieve high heating and cooling energy savings when integrated with building systems. Proper integration of these systems can contribute to the efficiency of heating and cooling energy uses as well as improvement of daylight in nearly any buildings, and in particular in highly-glazed and lightweight buildings, which are becoming popular worldwide. This study aims to investigate the optimal application of Phase Change Materials (PCMs), natural ventilation, and solar shading systems in maximizing energy conservation and comfort level in a highly-glazed study room located in a cold climate. For this purpose, a whole-building energy model of the Stanley Pauley Engineering Building (SPEB) is developed using a building performance simulation (BPS) tool, EnergyPlus. In order to gain confidence in the SPEB model, its outputs are compared against the SPEB model developed in an IES tool. The discrepancies of around 2.1% and 1.7% between the predictions of the total energy consumption and energy use intensity, respectively, suggest excellent agreement between the two models. Afterward, the SPEB model is used to examine, test, and analyze different design strategies for optimal application and use of PCM, shading, and natural ventilation. This is accomplished by using sophisticated Energy Management System (EMS) within the EnergyPlus as well as coupling the SPEB model with the programing language MATLAB. A case study in this research was a graduate study room located on the top floor of the SPEB. The study concluded that the integration of PCM28 with the hydronic radiant floor system significantly reduces the annual heating and total energy demand by around 24% and 19%, respectively. Also, the economic analysis showed that the application of PCM-enhanced radiant floor, when incorporated with a thin layer of insulation, could recover the initial investment within 5 to 10 years, which indicates a high economic value and appears to be cost-effective. Furthermore, the findings from the optimal integration of passive cooling systems show that an integrated approach for automatic control of shading is more efficient compared to the individual strategies and can reduce the cooling and heating energy demand by around 20% and 5.6%, respectively.