The Boreal Owl (Aegolius funereus) is a nocturnal forest-dwelling species widely distributed throughout the world. One of the least studied and most southerly populations of this species lives in the Pyrenees Mountains. This population, 500–600 pairs, probably suffered a slight decline during recent decades due to forestry management practices. The use of nest boxes may become necessary to protect this species in southern Europe. The objective of this study was to establish a standard protocol for nest-box installation, based on the analysis of occupation rates of nest boxes installed during the last 20 yr and the comparison of reproductive data for nest boxes and natural nest cavities. Our results indicated that nest boxes should be installed at high elevations (above 2000 m asl), below 4 m aboveground, and preferably facing south or southeast. We also found that most territories are located where maximum July temperatures are <17°C, which suggests that increasing temperatures due to climate change may have a negative effect on this population.