High-latitude terrestrial ecosystems are key components in the global carbon cycle. The Northern Circumpolar Soil Carbon Database (NCSCD) was developed to quantify stocks of soil organic carbon (SOC) in the northern circumpolar permafrost region (a total area of 18.7 × 106 km2). The NCSCD is a geographical information system (GIS) data set that has been constructed using harmonized regional soil classification maps together with pedon data from the northern permafrost region. Previously, the NCSCD has been used to calculate SOC storage to the reference depths 0–30 cm and 0–100 cm (based on 1778 pedons). It has been shown that soils of the northern circumpolar permafrost region also contain significant quantities of SOC in the 100–300 cm depth range, but there has been no circumpolar compilation of pedon data to quantify this deeper SOC pool and there are no spatially distributed estimates of SOC storage below 100 cm depth in this region. Here we describe the synthesis of an updated pedon data set for SOC storage (kg C m−2) in deep soils of the northern circumpolar permafrost regions, with separate data sets for the 100–200 cm (524 pedons) and 200–300 cm (356 pedons) depth ranges. These pedons have been grouped into the North American and Eurasian sectors and the mean SOC storage for different soil taxa (subdivided into Gelisols including the sub-orders Histels, Turbels, Orthels, permafrost-free Histosols, and permafrost-free mineral soil orders) has been added to the updated NCSCDv2. The updated version of the data set is freely available online in different file formats and spatial resolutions that enable spatially explicit applications in GIS mapping and terrestrial ecosystem models. While this newly compiled data set adds to our knowledge of SOC in the 100–300 cm depth range, it also reveals that large uncertainties remain. Identified data gaps include spatial coverage of deep (> 100 cm) pedons in many regions as well as the spatial extent of areas with thin soils overlying bedrock and the quantity and distribution of massive ground ice. An open access data-portal for the pedon data set and the GIS-data sets is available online at http://bolin.su.se/data/ncscd/. The NCSCDv2 data set has a digital object identifier (doi:10.5879/ECDS/00000002).