The Western Siberia Lowland (WSL), the world's largest permafrost peatland, is of importance for understanding the high-latitude carbon (C) cycle and its response to climate change. Warming temperatures increase permafrost thaw and production of greenhouse gases. Also, permafrost thaw leads to the formation of lakes which are hotspots for atmospheric C emissions. Although lakes occupy ~6% of WSL, lake C emissions from WSL remain poorly quantified. Here we show high C emissions from lakes across all permafrost zones of WSL. The C emissions were especially high in shoulder seasons and in colder permafrost-rich regions. The total C emission from permafrost-affected lakes of WSL equals ~12 ± 2.6 Tg C yr-1 and is 2-times greater than region's C export to the Arctic coast. The results show that C emission from WSL lakes is a significant component in the high-latitude C cycle, but also suggest that C emission may decrease with warming.