With the rising environmental consciousness, emission pollution has become one of the major concerns of the maritime industry, which is the artery of international trade. To handle the significant cost increase resulting from stringent emission regulations, ship operators have adopted multiple methods, including operational and technical methods. Scrubbers are a mature and effective technology that can reduce sulfur dioxide and particulate matter emissions by cleaning the exhaust gases before emitting them. However, the existing literature regarding the operation of scrubbers does not consider the prohibition of open scrubber usage in the vicinity of certain ports or the variable costs of using scrubbers. Therefore, this study explores the fleet scrubber installation and utilization problem, considering sulfur emission control areas, marine fuel switching, and open-scrubber-prohibited areas. A mixed-integer nonlinear model was developed to formulate and address the problem. Numerical experiments and sensitive analyses based on practical data were conducted to validate the originally proposed model and show the effectiveness of this technology under various scenarios. The results indicated that the operational cost was effectively reduced by using scrubbers, compared to not using them. Additionally, the disparity between total costs with and without scrubbers was significant, regardless of the sailing speed and proportion of the regulation areas. It was also proven that spreading the scrubber installation work over several years will relieve financial pressures due to scrubber investment and thus obtain a better installation plan.