Ice-core records from the interior of the Greenland ice sheet suggest widespread thinning during the Holocene. However, the recurring underestimation of this thinning in numerical models raises concerns about both the veracity of such reconstructions and the reliability of glaciological models. Recent work suggests the 8000-year-old Northeast Greenland Ice Stream (NEGIS), including a now-extinct northern tributary, may have been an early influence on Greenland ice-sheet dynamics. Yet, the inaccurate reproduction of NEGIS-like dynamics in most models hampers investigation of whether this feature played a role in Holocene ice-sheet thinning. Here we show that grounding-line retreat in northeast Greenland triggers elevation changes at the northern summit via ice-dynamic effects modulated by the paleo NEGIS system. In our simulations, fast ice-stream flow caused by transiently imposed reduced basal shear stress following the northeast retreat explains 55% (± 18%) of the estimated ice thinning, showing that ice-stream dynamics is one of the main drivers of the NGRIP Holocene surface elevation drop. Our findings show that the ice-flow in northeast Greenland plays a large role in ice-surface elevation changes in central Greenland.