Polar ice-core records suggest that an arctic or boreal source was responsible for more than 30% of the large increase in global atmospheric methane (CH4) concentration during deglacial climate warming; however, specific sources of that CH4 are still debated. Here we present an estimate of past CH4 flux during deglaciation from bubbling from thermokarst (thaw) lakes. Based on high rates of CH4 bubbling from contemporary arctic thermokarst lakes, high CH4 production potentials of organic matter from Pleistocene-aged frozen sediments, and estimates of the changing extent of these deposits as thermokarst lakes developed during deglaciation, we find that CH4 bubbling from newly forming thermokarst lakes comprised 33 to 87% of the high-latitude increase in atmospheric methane concentration and, in turn, contributed to the climate warming at the Pleistocene-Holocene transition.