Momentum is growing for the management of coral reefs as a strategy to reduce climate risks in tropical coastlines. Yet, quantification of the life-time costs, impacts, and benefits remains limited. This study provides one of the first rigorous, spatially explicit, regional-scale Benefit:Cost Analyses (BCA) for coral reef restoration and was designed to meet the BCA requirements of major hazard mitigation funding and programs. This study simulates coastal flooding using a hydrodynamic model under different scenarios representing current coral reef conditions, reef degradation, and reef restoration. These coastal flood maps are used to estimate socioeconomic damages, which are included in a BCA to assess cost-effectiveness and priority areas for coral reef conservation and restoration. The United States Virgin Islands is used as a case study given recent impacts from storms and their new policy that declares reefs as natural infrastructure. The results show that flood risk across the islands of Saint Croix, Saint John, and Saint Thomas is $51.4 million USD per year. Annually, coral reefs prevent flood damages to 481 people and $43.6 million USD of infrastructure, which represents 87 % of the flood risk. These results identify the communities that could receive the greatest benefits from coral conservation and restoration, which overlap significantly. Coral reef restoration is found to be a cost-effective strategy for flood mitigation although how reefs are restored matters. Hybrid coral reef restoration provides greater flood mitigation benefits than ecological restoration, but its cost-effectiveness is overall lower given its greater costs. Many coastal areas have benefit:cost ratios exceeding 1.5, which complies with typical government agencies’ requirements for accessing hazard mitigation funds. This valuation framework helps provide rigorous regional-scale quantification of nature-based coastal protection solutions for coastal risk management decisions.