Background: Malaria is an insect-borne infectious disease that spreads through bites from infected Anopheles mosquitos. The disease seriously endangers human health and economic development. The study focuses on Fujian Province, China, which entered the final stage of malaria elimination stage in 2005. In order to understand the costs and benefits of malaria monitoring measures during the elimination stage, the health economics of the monitoring measures should be examined. Methods: Data on the number of cases during the malaria elimination stage (2005–2019) in Fujian Province were collected and sorted. The basic economic data were obtained from the Fujian Statistical Yearbook. Based on the fundamental theories in health economics, a cost-benefit analysis was conducted based on the data. Specifically, the cost of monitoring measures during the malaria elimination stage was calculated by economic cost and compared to the benefits, which were quantified based on economic and social benefits of the monitoring measures.Results: The total cost of monitoring measures in the malaria elimination stage was estimated at 607,878,783.36 yuan (USD 87,534,544.80). The components of the total cost were: case detection and treatment, which accounted for 66.62% of costs, health education with 13.31%, epidemic monitoring, 10.05%, supervision and assessment, 5.15%, and training and meetings took 4.87%. The total benefit of the monitoring measures in the malaria elimination stage was valued at about 116,123,417,911.81 yuan (USD 16,721,772,179.30). Direct economic benefit accounted for 22.61% of the total, while the social benefit was 77.39%. The cost-benefit analysis of the malaria elimination stage showed that the net benefit of monitoring measures was about 115,515,539,128.45 yuan (USD 16,634,237,634.50) and the benefit-cost ratio was 191.03. The monitoring cost for residents was 1.08 yuan (USD 0.16) per capita, and the benefit for residents was 206.12 yuan (USD 29.68) per capita. Conclusions: The monitoring measures conducted in the malaria elimination stage are a highly cost-effective intervention for reducing the negative impact of malaria in Fujian Province. Over the past 15 years, malaria control work has achieved excellent economic and social benefits in Fujian and the work should continue. The framework and results of this study conform to the principles of health economics and have a reference value for current malaria monitoring practices.