Methane (CH4) emissions from the boreal and arctic region are globally significant and highly sensitive to climate change. There is currently a wide range in estimates of high-latitude annual CH4 fluxes, where estimates based on land cover inventories and empirical CH4 flux data or process models (bottom-up approaches) generally are greater than atmospheric inversions (top-down approaches). A limitation of bottom-up approaches has been the lack of harmonization between inventories of site-level CH4 flux data and the land cover classes present in high-latitude spatial datasets. Here we present a comprehensive dataset of small-scale, surface CH4 flux data from 540 terrestrial sites (wetland and non-wetland) and 1247 aquatic sites (lakes and ponds), compiled from 189 studies. The Boreal–Arctic Wetland and Lake Methane Dataset (BAWLD-CH4) was constructed in parallel with a compatible land cover dataset, sharing the same land cover classes to enable refined bottom-up assessments. BAWLD-CH4 includes information on site-level CH4 fluxes but also on study design (measurement method, timing, and frequency) and site characteristics (vegetation, climate, hydrology, soil, and sediment types, permafrost conditions, lake size and depth, and our determination of land cover class). The different land cover classes had distinct CH4 fluxes, resulting from definitions that were either based on or co-varied with key environmental controls. Fluxes of CH4 from terrestrial ecosystems were primarily influenced by water table position, soil temperature, and vegetation composition, while CH4 fluxes from aquatic ecosystems were primarily influenced by water temperature, lake size, and lake genesis. Models could explain more of the between-site variability in CH4 fluxes for terrestrial than aquatic ecosystems, likely due to both less precise assessments of lake CH4 fluxes and fewer consistently reported lake site characteristics. Analysis of BAWLD-CH4 identified both land cover classes and regions within the boreal and arctic domain, where future studies should be focused, alongside methodological approaches. Overall, BAWLD-CH4 provides a comprehensive dataset of CH4 emissions from high-latitude ecosystems that are useful for identifying research opportunities, for comparison against new field data, and model parameterization or validation. BAWLD-CH4 can be downloaded from https://doi.org/10.18739/A2DN3ZX1R (Kuhn et al., 2021).