Studying current and future geographic distribution is essential for conserving endangered species such as the Boreal Owl and Eurasian Pygmy Owl. The main aim of this study was to determine the potential distribution of both species in the Balkan Peninsula by using spatial distribution models (SDMs) in MaxEnt. We used data from field surveys, the scientific and grey literature, and an online database. We considered the current time and two future periods, 2041–2060 and 2061–2080. For future periods, we included different climate scenarios (SSP 126, 245, 370, and 585) in studying the potential geographic distribution of both species. We identified two types of potential future refugia for species: in situ and ex situ. Our study shows the highly suitable area for the Boreal Owl increased during the 2041–2060 period compared with the current area in all scenarios, except in SSP 585. However, during the 2061–2080 period, the highly suitable areas contracted. For the Eurasian Pygmy Owl, highly suitable areas decreased during 2041–2060, but during the 2061–2080 period, it was larger than the current area. Our study is of importance for conservation and preserving areas of potential distribution and refugia for Boreal and Eurasian Pygmy Owls in the face of climate change.