Abstract Selection of clean technology options requires systematic evaluation based on multiple criteria which are often conflicting. The optimal choice should consider not just technical performance but also the economic, environmental and social aspects of technologies. Furthermore, the interdependencies of these aspects should also be considered. The decision-maker often needs to make explicit trade-offs while ranking the alternatives. In addition, data gaps and imprecise information that are typical when dealing with emerging technologies make conventional methods ineffective. This work thus proposes a Stochastic Fuzzy Analytic Hierarchical Network Process decision model to address the complexity and uncertainty involved in the clean technology selection process. This method first decomposes the problem into a hierarchical network structure, and then derives the probability distribution of the priority weights needed for ranking. The capabilities of the methodology are demonstrated with three case studies, involving the comparison of different carbon nanotube synthesis methods, nutrient removal treatment technology options for municipal wastewater, and low-carbon electricity sources in the Philippines.