Invasion by non-native species is one of the major threats to the conservation of biodiversity and to the provision of ecosystem services by protected areas. Invasive species often co-occur in protected areas, represented by sparse, isolated individuals or populations in different stages in the process of invasion. Species invasiveness, habitat invasibility and impact also differ between ecosystems, so the risk of invasion varies. Besides, prioritization is required due to constraints on time, financial and other resources. Priority-setting is therefore key to help protected area managers invest efforts on biological invasions that offer the best chances of producing large-scale positive results at the lowest cost possible. A priority-setting scheme for the control of invasive non-native species in natural areas is presented in this paper. The scheme, based on field observations of species occurrences, was applied to the Itatiaia National Park (Brazil). Priorities are calculated from a combination of three criteria attributed to each occurrence: species risk of invasion considering local ecosystems, invasion stage, and species frequency. Data collected in the field in the Itatiaia National Park were used to calculate priorities for 50 non-native species (six animals and 44 plants) in four locations in the Park. The highest priorities were attributed to species of high risk in an early stage of invasion occurring in one site, whereas a few widespread species of low risk were given lower priority. The scheme has proven functional for setting priorities for the control of non-native species in the Itatiaia National Park and in many other protected areas in Brazil.