Anthropogenic global warming and deforestation are significant drivers of the global biodiversity crisis. Ectothermic and viviparous animals are especially vulnerable since high environmental temperatures can impair embryonic development, but we lack knowledge about these effects upon Neotropical organisms. Here, we estimate how much of the current area with suitable habitats overlaps with protected areas and model the combined effects of climate change and deforestation on the geographic distribution of the viviparous Neotropical lizard Notomabuya frenata (Scincidae). This species ranges in Brazil, Argentina, Paraguay, and Bolivia. We use environmental and physiological variables (locomotor performance and hours of activity) to predict suitable present and future areas, considering different scenarios of greenhouse gas emissions and deforestation. The most critical predictors of habitat suitability were isothermality (i.e., the ratio between mean diurnal temperature range and annual temperature range), precipitation during winter, and hours of activity under lower thermal extremes. Still, our models predict a contraction of suitable habitats in all future scenarios and the displacement of these areas towards eastern South America. In addition, protected areas are not enough to ensure suitable habitats for this species. Our findings highlight the vulnerability of tropical and viviparous ectotherms and suggest that even widely distributed species, such as N. frenata, may have their conservation compromised shortly due to the low representativeness of their suitable habitats in protected areas combined with the synergistic effects of climate change and deforestation. We stress the need for decision‐makers to consider the impact of range shifts in creating protected areas and managing endangered species.