This dataset provides gridded estimates of soil CO2 flux (g C m-2 d-1) for the winter non-growing season (NGS) across pan-Arctic and Boreal permafrost regions (>49 Deg N), at 25 km spatial resolution. The data are the daily average flux over a monthly period for two climate periods: the baseline climate period represents 2003-2018 and the future climate scenarios period represents 2018-2100 under Representative Concentration Pathways (RCP) 4.5 and 8.5. The data were produced by applying a Boosted Regression Tree machine learning approach to create gridded estimates of emissions based on in situ observations of NGS fluxes provided in a related dataset. The resulting monthly average flux data records can be used to calculate annual NGS soil CO2 flux budgets from 2003-2100.