This dataset provides global gridded information on lake surface area and open water CH4 emissions at a resolution of 0.25-degree x 0.25-degree for an annual climatology representative of the average conditions from 2003 to 2015. A compilation of flux data from 575 individual lake systems and 893 aggregated flux values were used, and each flux measurement was classified into one of seven ecoclimatic types. Ice-cover-regulated emission seasonality was derived from satellite microwave observations of ice cover phenology and freeze-thaw dynamics. Global lake area was determined from the merger of HydroLAKES and Climate Change Initiative Inland-Water (CCI-IW) remote-sensing data, and lakes were classified into ecoclimatic regions to facilitate linking these types with ecosystem-specific CH4 measurements in the flux compilation. Exploratory estimates of fluxes associated with ice melt and with spring and fall water-column turnover are also included. The data are provided in NetCDF format.