Abstract Background Stoma closure is associated with a high incidence of incisional hernia, which not only impose significant costs on the healthcare system but also negatively impact patient’s overall health. Prophylactic mesh placement for stoma closure has proven effective in preventing these hernias; however, its broader implementation is limited primarily by cost-effectiveness concerns. Methods We carried out an economic evaluation to assess the cost-effectiveness of the use of selective prophylactic mesh (high-risk patients) in patients who underwent stoma closure, using data from a systematic review and meta-analysis that evaluated risk factors, and another systematic review and meta-analysis that evaluated the effectiveness of prophylactic mesh. Results Our study showed that selective strategy offers an alternative with a lower incremental cost and comparable, although lower effectiveness. While prophylactic mesh placement in all patients has a higher incremental cost, it also has higher effectiveness. Nevertheless, the incremental cost does not exceed the threshold established in our setting of 2 times the GDP per capita. Conclusion The use of prophylactic mesh for the closure of all stomas is a strategy that should be implemented and performed with a prosthetic mesh to be a cost-effective strategy.