Green roof systems have been suggested to ease the growing urban environmental problems resulting from rapid urbanization. However, the irrigation of green roofs heavily depends on using precious potable water and consequently generates negative environmental effects. Rainwater has been recommended to address this dilemma, but the design method has not been well developed. In this study, the major design factors of a rainwater harvesting system for green roof irrigation systems are examined, and a simulation-based mathematical model is established to elucidate the correlation between tank volume and system performance. The optimal system design and probability distribution of the potable water replacement rate are also discussed on the basis of a case study of a university building in Keelung, Northern Taiwan. The results show that the optimal tank volume, potable water replacement rate, and probability of exceedance are 9.41 m3, 92.72%, and 88.76% (±1SD), respectively. In addition, the economic performance is identified to be feasible. Hence, the design method has been verified to be a useful tool to ease the urban environmental issues.