The British red squirrel population has dramatically declined in the last years. The survival of the species in the UK may depend on the careful selection and management of suitable habitats. A deep understanding of its habitat requirements is therefore crucial for an effective conservation action. Available data, however, is often too coarse in spatial resolution for practical use. The aim of this study was to test the applicability of species distribution modelling for mapping red squirrel habitat suitability at a fine scale. A sampling campaign was designed and implemented in Queen Elizabeth Forest Park (Scotland) in order to collect data relating to forest structural characteristics and squirrel occurrence. Later regression analysis showed the importance of forest structural features in red squirrel presence. The relationship between forest structural variables and different remote sensing vegetation indices was also investigated in order to extrapolate them to the whole study area. Canopy cover was modelled with some accuracy using NDVI as the only explanatory variable. Finally, red squirrel habitat suitability was modelled using a maximum entropy approach. The results of this study suggested that there is a hierarchy in which tree age, tree species composition and forest structure, in this order, have an influence in squirrel habitat preference. Old forests were strongly linked with suitable squirrel habitat. The relatively low model’s predictive power suggested that fine-scale habitat mapping is particularly sensitive to sampling biased input data. The study identifies some critical points to take into account in future modelling studies and encourage further research in the area.