The design practice of the government schools has undergone several changes, which are also expected to influence their thermal and operational performance. Under the current economic situation, the schools are obliged to reduce the operational cost, especially after implementing the new cost-reflective tariff (CRT) structure in 2017, which removes the governmental subsidy from high energy consumers. The concept of net-zero energy schools has been proposed as a critical step to achieve self-sustained buildings where passive, active, and renewable energy systems are considered. Therefore, the aim of this research was to develop an optimal design for a net-zero energy school in three representative climates of Oman; hot-humid climate represented by Muscat, hot-dry climate represented by Nizwa, and moderate climate represented by Salalah. A multiphase methodology was followed, including data collection of typical schools from the Ministry of Education, collection of the capital cost of passive and active systems from an approved list of contractors, an energy audit of a typical school, and fieldwork measurements. A post-basic school with 20 classrooms located in a hot-humid climate was selected as a school building prototype. The school was modeled in the DesignBuilder software, a whole-building simulation package. The model was validated using the fieldwork measurements, which was used to analyze the school performance. The base case model shows that energy use intensity (EUI) is 142.5 kWh/m2 , which is considered slightly higher compared to other schools in hot regions, typically between 84 to 93 kWh/m2 . The research revealed that the passive and active design strategies are economically not feasible due to high capital cost, and therefore savings in energy consumption and savings in energy cost were considered as performance indicators. In general, the passive design strategies have shown moderate potential in reducing energy consumption and energy cost in all climates. On the other hand, active strategies such as LED lights, lighting control, and air conditioning systems have shown more potential in reducing energy consumption and energy cost. The optimal design for the three climates was then determined. The research indicated that wall and roof insulations with a 50 mm thickness should be used in hot climates but are not important in a moderate climate. High-performance double clear low-E glazing with solar coatings is recommended in all climates. Windows shadings are not recommended when daylighting is harvested since it may hinder the savings in artificial lights. LED lights with dimming and variable refrigerant flow (VRF) air conditioning are recommended active systems for all climates. The optimal school design has reduced the energy consumption by 28.53%, 27.90%, and 25.14% in Muscat, Nizwa, and Salalah, respectively. The savings in energy costs were 29.9%, 29.5%, and 25.9% in Muscat, Nizwa, and Salalah, respectively. PV systems were then integrated into the optimal school design to achieve net-zero energy status. When integrating the PV systems and the optimal design strategies, the energy savings for the school may reach up to 68.73%, 68.57%, and 65.76% in Muscat, Nizwa, and Salalah, respectively, with the rest being injected into the national grid. Similar values were also achieved for the reduction in the CO2 emissions and the energy cost, achieving carbon-neutral and zero-cost energy schools.