Road mortality affects natural populations worldwide. Although the effects of road mortality are often documented, studies assessing the impact of road mortality on the viability of the affected populations are not so common. In fact, road mortality data are often limited to a small number of years from which it is difficult to build statistical models to assess the impact of road mortality on population trends, including the probability of extinction. In the last decades several studies have reported a considerable decline in barn owl (Tyto alba) populations attributed mainly to land use change and to the expansion of the road network to accommodate traffic growth. For instance, road monitoring programs show high road mortality rates ranging from 0.07 owls/km/year to 2.61 owls/km/year. We developed a stochastic, age-structured model to evaluate the impact of road-kills on barn owl populations and their risk of extinction. Using this model we identified the range of parameters that are most likely to apply to a population in southern Portugal and assessed how road mortality has affected this population. Three important results are: the number of individuals of the barn owl population exhibits high intra and inter-annual variability, even an annual road mortality rate of 5% reduces barn owl populations to half of their original size, and probability of extinction increases dramatically when annual road mortality exceeds 30% and it is largely independent of the original population size. Although simulations seem to show that road mortality is still below the values for which there is risk of extinction, we recommend authorities to closely monitor the owls’ numbers temporal trends and to take the necessary measures to reduce road mortality.