Marine protected areas (MPAs) are an increasingly popular, but debated, management strategy to conserve marine biodiversity and ensure sustainable human use of the oceans. Economic studies can contribute to the debate about MPAs as a management option by evaluating their benefits and costs to society. In this paper, we outline how to evaluate the economic benefits and costs of MPAs and provide examples from the literature to demonstrate the methods described. We review challenges and opportunities of different economic methods. One key challenge is to meaningfully compare market and non‐market benefits of MPAs—this comparison is complicated by the scarcity of studies that quantify the non‐market benefits of MPAs. Another key challenge is to quantify how the value of marine areas may change with and without MPAs. Costs are often easier to estimate than benefits, but some costs—such as maintenance and compliance costs—are rarely recognized. Analytical choices will influence the identified economic costs and benefits of MPAs. For example, the spatial extent of analyses will influence what changes in underlying ecological processes are captured and conclusions about the equitable distribution of costs and benefits across society. For these reasons, it is important that managers are aware of the challenges and opportunities described here, so that they can obtain and use the best‐quality economic information to guide decision making about MPAs.