Protected areas are essential conservation tools for mitigating the rapid decline of biodiversity. However, climate change represents one of the main challenges to their long‐term effectiveness, as it induces rapid changes in the geographical distribution of many species. We used ecological niche modelling to predict the impacts of climate change on the distribution of five endemic owls in the Atlantic Forest and evaluated the effectiveness of the protected areas network for their conservation. The results indicate that the protected areas network is currently effective in terms of representativeness for most species; however, there will be a decline for all species in the coming decades because of climate change. We found that the ecoregions in the northern part of the Atlantic Forest will experience a higher loss of species, whereas those ecoregions in the southern part will be important stable climatic refuges in the future. Therefore, we emphasize the need to complement the network of protected areas to increase their representativeness in the distribution of species that will be affected by climate change, reducing species loss and increasing connectivity between suitable areas. We hope the results presented herein will serve as a basis for decision‐makers to re‐evaluate and improve current conservation policies and decisions in order to address the challenges posed by climate change and secure the survival of these species.