Mountain protected areas (PAs) aim to preserve vulnerable environments and at the same time encourage numerous outdoor leisure activities. Understanding the way people use natural environments is crucial to balance the needs of visitors and site capacities. This study aims to develop an approach to evaluate the structure and use of designated skiing zones in PAs combining Global Positioning System (GPS) tracking and analytical methods based on graph theory. The study is based on empirical data (n = 609 GPS tracks of backcountry skiers) collected in Tatra National Park (TNP), Poland. The physical structure of the entire skiing zones system has been simplified into a graph structure (structural network; undirected graph). In a second step, the actual use of the area by skiers (functional network; directed graph) was analyzed using a graph-theoretic approach. Network coherence (connectivity indices: β, γ, α), movement directions at path segments, and relative importance of network nodes (node centrality measures: degree, betweenness, closeness, and proximity prestige) were calculated. The system of designated backcountry skiing zones was not evenly used by the visitors. Therefore, the calculated parameters differ significantly between the structural and the functional network. In particular, measures related to the actually used trails are of high importance from the management point of view. Information about the most important node locations can be used for planning sign-posts, on-site maps, interpretative boards, or other tourist infrastructure.