Many shipping companies have started using scrubbers in their fleet to eliminate sulfur emissions from ships, per IMO (International Maritime Organization) rules. Before and during the scrubbers’ selection, the scrubbers’ operational failures have also started to appear and cause serious concerns. In this study, classified scrubber types are explained and open type, closed type, and hybrid scrubber systems are evaluated. To contribute to this gap in the literature, scrubber failures were identified, five experts with different perspectives were consulted, and the most common and critical malfunctions were evaluated with the fuzzy best–worst method (F-BWM) and fuzzy technique for order preference by similarity to an ideal solution (F-TOPSIS). F-BWM was used to determine the importance weights of the risk parameters used in evaluating failures since it provides fewer comparisons among pairwise comparison–based decision-making methods and a more consistent judgment in the evaluation. F-TOPSIS, on the other hand, was used to determine the final priority scores of the scrubber failures, taking into account the risk parameter weights obtained in the first stage. It has been preferred due to its easy to useness and based on its closeness to the ideal solution and applicability to risk and failure analysis problems. Considering all different systems in general, important issues such as collection efficiency, sulfur emission problem, abrasion, leakages, pump failures, heat exchanger failures, air fan sealing failures, sensors and failures in monitoring the whole system have been investigated. Results show that too high axial velocity for separator and flooded separator, too high solids concentration in recirculation liquid (SF2), piping leakages (SF5), poor quality or inappropriate consumables and chemicals (SF11), and feed circulation pump problems (SF6) are found to be the most important problems among thirteen failures.