West Antarctica consists of several tectonically diverse terranes, including the West Antarctic Rift System, a topographic low region of extended continental crust. In contrast, the adjacent Marie Byrd Land and Ellsworth‐Whitmore mountains crustal blocks are on average over 1 km higher, with the former dominated by polygenetic shield and stratovolcanoes protruding through the West Antarctic ice sheet and the latter having a Precambrian basement. The upper mantle structure of these regions is important for inferring the geologic history and tectonic processes, as well as the influence of the solid earth on ice sheet dynamics. Yet this structure is poorly constrained due to a lack of seismological data. As part of the Polar Earth Observing Network, 13 temporary broadband seismic stations were deployed from January 2010 to January 2012 that extended from the Whitmore Mountains, across the West Antarctic Rift System, and into Marie Byrd Land with a mean station spacing of ~90 km. Relative P and S wave travel time residuals were obtained from these stations as well as five other nearby stations by cross correlation. The relative residuals, corrected for both ice and crustal structure using previously published receiver function models of crustal velocity, were inverted to image the relative P and S wave velocity structure of the West Antarctic upper mantle. Some of the fastest relative P and S wave velocities are observed beneath the Ellsworth‐Whitmore mountains crustal block and extend to the southern flank of the Bentley Subglacial Trench. However, the velocities in this region are not fast enough to be compatible with a Precambrian lithospheric root, suggesting some combination of thermal, chemical, and structural modification of the lithosphere. The West Antarctic Rift System consists largely of relative fast uppermost mantle seismic velocities consistent with Late Cretaceous/early Cenozoic extension that at present likely has negligible rift related heat flow. In contrast, the Bentley Subglacial Trench, a narrow deep basin within the West Antarctic Rift System, has relative P and S wave velocities in the uppermost mantle that are ~1% and ~2% slower, respectively, and suggest a thermal anomaly of ~75 K. Models for the thermal evolution of a rift basin suggest that such a thermal anomaly is consistent with Neogene extension within the Bentley Subglacial Trench and may, at least in part, account for elevated heat flow reported at the nearby West Antarctic Ice Sheet Divide Ice Core and at Subglacial Lake Whillans. The slowest relative P and S wave velocity anomaly is observed extending to at least 200 km depth beneath the Executive Committee Range in Marie Byrd Land, which is consistent with warm possibly plume‐related, upper mantle. The imaged low‐velocity anomaly and inferred thermal perturbation (~150 K) are sufficient to support isostatically the anomalous long‐wavelength topography of Marie Byrd Land, relative to the adjacent West Antarctic Rift System.