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Temporary no-take zones (NTZs) are increasingly introduced in Sweden as a fisheries management tool to restore populations of specific target species. This paper presents a cost-benefit analysis of two real case temporary NTZs closed during a 5–6 year period in the coastal zone of the Baltic Sea, using scenario analysis to account for uncertainty in both the biological and economic effects. A sensitivity analysis was added for certain key parameters. The results of the cost-benefit analyses for the two NTZs are positive in all scenarios relating to the most realistic case of no opportunity costs, i.e., assuming that all fishing activity could be relocated to adjacent areas without cost during the closed period. As an extreme case comparison, full opportunity costs were included, assuming that no fishing activity could be relocated to other areas during the closed period. One of the NTZs then exhibited a negative net result for most scenarios. For the other area the net result was positive even when the maximum opportunity costs of temporary lost fishing opportunities were included, largely depending on the strong positive change in the value of commercial fishing. By demonstrating potential costs and benefits of using temporary no-take zones in fisheries management this study may contribute to policy making, as well as to creating acceptance from stakeholder groups that incur short-term costs from closing areas to fishing.