The number of invasive non-native species (INNS) has been increasing in Brazilian protected areas (PAs) in the last decades, even though Brazil is close to reaching the Global Biodiversity Framework Target of having at least 30% of the territory conserved in PAs. The main aim of our study is to identify spatial patterns and factors that describe the number of INNS in federal and state protected areas in Brazil. We integrated and standardized three sources of occurrences of INNS in federal and state PAs with a new database built for this study based on occurrences reported in 424 management plans (MP). A generalized linear model was used to assess the factors that best describe the number of INNS in PA using biome, year of PA creation, PA area, PA group, and PA category as fixed effects. We compiled 5,631 occurrences of 150 invasive animals, 179 invasive plants, four ferns, three protists, one alga, and one bryophyte. Protected areas with the highest number of INNS are concentrated along the coast, in the Atlantic Forest biome, especially in the south and southeast of Brazil. Biome, PA category, and PA year of creation were the most important variables in the model. We expect our results to show the magnitude of biological invasions in Brazilian PAs and we provide baseline data and recommendations to be used as reference for the development of policies and management actions at regional and local levels, thus contributing to the achievement of KMGBF targets.