China is the world's largest emitter of greenhouse gases (GHGs) and the agricultural sector in China is responsible for 17–20% of annual emissions and 62% of total freshwater use. Groundwater abstraction in China has increased rapidly from 10 km3 yr−1 in the 1950s to more than 100 km3 yr−1 in the 2000s, such that roughly 70% of the irrigated area in northern China is now groundwater-fed. Pumping of water for irrigation is one of the most energy consuming on-farm processes; however, to date this source of GHG emissions in China and elsewhere has been relatively neglected. We derive the first detailed estimate of GHG emissions from groundwater pumping for irrigation in China, using extensive village survey data from 11 provinces, broadly representative of the situation during the mid-2000s. The 11 provinces cover roughly half of China's irrigated cropland and we upscale to the national level using government statistics for the remaining 20 provinces. Our results show emissions of 33.1 MtCO2e, just over half a per cent of the national total. Groundwater abstraction represents an important source of GHG emissions that has been rapidly increasing and which at present is largely unregulated. Water scarcity in China is already driving policies to improve water conservation. These results suggest that significant potential exists to promote the co-benefits of water and energy saving in order to meet national planning targets.