This study presents the geodetic mass balance of Kanchenjunga Glacier, one of the largest debris-covered glaciers in the easternmost Nepal Himalaya, which possesses a negative mass balance of −0.18 ± 0.17 m w.e. a −1 for the 1975–2010 study period, estimated using digital elevation models (DEMs) generated from Hexagon KH-9 and ALOS PRISM stereo images. Accurate DEMs, with a relative uncertainty of ±5.5 m, were generated from the intensive and manual editing of triangulated irregular network (TIN) models on a stereo MirrorTM/3D Monitor. The glacier ice-flow velocity field was also calculated using a feature-tracking method that was applied to two ALOS orthoimages taken in 2010. The elevation differences between the two DEMs highlight considerable surface lowering across the debris-covered area, and a slight thickening in the accumulation area of Kanchenjunga Glacier between 1975 and 2010. The magnitude and gradient of surface lowering are similar among the six glacier tributaries, even though they are situated at different elevations, which may reflect variations in the ice-flow velocity field. The pattern of surface lowering correlates well with the ice-flow velocity field over the debris-covered portion of the main tributary, suggesting that the glacier dynamics significantly affect surface lowering by altering the emergence velocity along the glacier, particularly in the compressive ablation area. Surface-lowering patterns partially correspond to the supraglacial pond area fraction of the glacier, with enhanced surface lowering observed in areas that possess a larger pond area fraction. These findings support the hypothesis that supraglacial ponds may intensify ice wastage and play a key role in the heterogeneous surface lowering of debris-covered glaciers. The estimated mass loss of Kanchenjunga Glacier is moderate compared with other debris-covered glaciers in neighboring Himalayan regions, which may be due to the lower pond area fraction of Kanchenjunga Glacier relative to other glaciers.