This dataset provides a synthesis of winter ( September-April) in situ soil CO2 flux measurement data from locations across pan-Arctic and Boreal permafrost regions. The in situ data were compiled from 66 published and 21 unpublished studies conducted from 1989-2017. The data sources (publication references) are provided. Sampling sites spanned pan-Arctic Boreal and tundra regions (>53 Deg N) in continuous, discontinuous, and isolated/sporadic permafrost zones. The CO2 flux measurements were aggregated at the monthly level, or seasonally when monthly data were not available, and are reported as the daily average (g C m-2 day-1) over the interval. Soil moisture and temperature data plus environmental and ecological model driver data (e.g., vegetation type and productivity, soil substrate availability) are also included based on gridded satellite remote sensing and reanalysis sources.