The fate of the vast stocks of organic carbon stored in permafrost of the Western Siberian Lowland, the world’s largest peatland, is uncertain. Specifically, the amount of greenhouse gas emissions from rivers in the region is unknown. Here we present estimates of annual CO2 emissions from 58 rivers across all permafrost zones of the Western Siberian Lowland, between 56 and 67° N. We find that emissions peak at the permafrost boundary, and decrease where permafrost is more prevalent and in colder climatic conditions. River CO2 emissions were high, and on average two times greater than downstream carbon export. We suggest that high emissions and emission/export ratios are a result of warm temperatures and the long transit times of river water. We show that rivers in the Western Siberian Lowland play an important role in the carbon cycle by degassing terrestrial carbon before its transport to the Arctic Ocean, and suggest that changes in both temperature and precipitation are important for understanding and predicting high-latitude river CO2 emissions in a changing climate.