Permafrost soils store large amounts of carbon. Warming can result in carbon release from thawing permafrost, but it can also lead to enhanced primary production, which can increase soil carbon stocks. The balance of these fluxes determines the nature of the permafrost feedback to warming. Here we assessed decadal changes in soil organic carbon stocks in the active layer—the uppermost 30 cm—of permafrost soils across Tibetan alpine regions, based on repeated soil carbon measurements in the early 2000s and 2010s at the same sites. We observed an overall accumulation of soil organic carbon irrespective of vegetation type, with a mean rate of 28.0 g C m−2 yr−1 across Tibetan permafrost regions. This soil organic carbon accrual occurred only in the subsurface soil, between depths of 10 and 30 cm, mainly induced by an increase of soil organic carbon concentrations. We conclude that the upper active layer of Tibetan alpine permafrost currently represents a substantial regional soil carbon sink in a warming climate, implying that carbon losses of deeper and older permafrost carbon might be offset by increases in upper-active-layer soil organic carbon stocks, which probably results from enhanced vegetation growth.