The Northeast Greenland Ice Stream (NEGIS) is an elongated feature extending ∼600 km into the interior of the Greenland Ice Sheet. Here, we investigate detailed subglacial topography along the length of the NEGIS to ascertain the characteristics of the ice stream bed. We use topographic analysis (hypsometry, spatial roughness and valley morphometry) to describe and demarcate three geomorphologically distinct regions. The upstream region, near the NEGIS onset, exhibits low roughness and a lack of valleys, indicating the likely presence of subglacial sediments. Downstream, roughness abruptly increases, with two wide subglacial troughs present in the middle region. In the downstream region, the topography displays smaller alpine-like valleys. We propose that these differences are attributable to changing geological provinces, which are poorly constrained in this area. The topography also has a distinct impact on ice stream geometry, as ice flow is generally preferentially steered through a trough. Whilst the upstream regime appears to have little effect on the location of the ice stream onset and shear margins, its low friction enables fast flow that propagates longitudinally upstream from the troughs. On the basis of our data, we argue that the NEGIS is more strongly influenced by basal topography than has been previously suggested.