Tropical deforestation is responsible for around one tenth of total anthropogenic carbon emissions, and tropical protected areas (PAs) that reduce deforestation can therefore play an important role in mitigating climate change and protecting biodiversity and ecosystem services. While the effectiveness of PAs in reducing deforestation has been estimated, the impact on global carbon emissions remains unquantified. Here we show that tropical PAs overall reduced deforestation carbon emissions by 4.88 Pg, or around 29%, between 2000 and 2012, when compared to expected rates of deforestation controlling for spatial variation in deforestation pressure. The largest contribution was from the tropical Americas (368.8 GgC y-1), followed by Asia (25.0 GgC y-1) and Africa (12.7 GgC y-1). Variation in PA effectiveness is largely driven by local factors affecting individual PAs, rather than designations assigned by governments.