<p>Creating cost-effective zero-energy buildings has recently been a big challenge for designers. The key factors in creating zero-energy buildings are the proper sizing of renewable and fossil fuel-based resources to provide the required demand capacity and the active/passive design of the buildings to reduce energy consumption. Rooftop photovoltaic (PV) panels are special devices that can impact both the energy production capacity in the building and the cooling energy reduction through the shading effect. The authors of this paper examine the risk-based, long-term planning of electrically isolated zero-energy buildings. This planning encompasses cost-effective envelope insulation, optimal sizing of energy resources, and management of operational costs throughout the planning period. Additionally, the authors address the risks associated with weather uncertainties by utilizing the Conditional Value at Risk (CVaR) methodology. The size of the rooftop photovoltaic (PV) system has a substantial influence on the design of the envelope insulation due to its shading effect on roof temperature. To achieve optimal sizing of energy resources alongside a cost-effective insulation design, a mixed-integer linear programming (MILP) approach is proposed. The study is conducted in two distinct regions of Iran: Kish Island and Zanjan, characterized by varying climatic conditions. The findings indicate that the utilization of rooftop PV systems can result in a cost reduction of $20,000 compared to ground-mounted PV systems; however, this approach necessitates a 4.5% increase in the area designated for rooftop PV panels.</p>