Compared to traditional building energy systems, the energy systems used in nearly/net zero energy buildings face more complex challenges due to highly uncertain characteristics associated with renewable energy systems. Traditional design methods of energy systems under deterministic conditions can lead to suboptimal solutions or failure in achieving building design targets. This study presents a review of design methodologies for flexible energy systems in nearly/net zero energy buildings under uncertainties. Firstly, the uncertainty sources associated with design are identified and the quantification methods of the identified uncertainties are discussed. Next, diverse techniques for modeling uncertain variables, and their advantages and disadvantages are reviewed. Thirdly, the whole design optimization process is analyzed from four perspectives, including modeling tools, optimization variables, objectives, and optimization techniques. Lastly, based on the insights from this review, several research gaps in characterizing and handling uncertainties, and modeling and optimizing energy systems in nearly/net zero energy buildings are identified, and recommendations for future research are suggested. This review study could provide valuable guidance in designing robust and flexible energy systems in nearly/net zero energy buildings, contributing to achieving carbon neutrality and environmental sustainability.