The crust and shallow upper mantle structure beneath the Upper Brahmaputra Valley, Indo-Burma Ranges, and Bengal Basin of Northeast India have been investigated based on receiver function (RF) analysis of teleseismic earthquakes recorded by 11 seismological stations. The study reveals a thin crust (∼35 km) beneath the Brahmaputra Valley (at JORH station) with a surface sedimentary layer of ∼4 km thick. The crustal thickness is observed to increase towards the north in the Himalaya (∼40 km at ZIRO and ITAN) and to the south (up to ∼46 km at KOHI). The crustal thickness near the Tripura fold-belt and Bengal Basin varies within ∼36–40 km. The study reveals the existence of a shallow mantle discontinuity (Hales discontinuity) at a variable depth range of ∼54–78 km characterized by a step increase (∼7.5–11 %) in shear wave velocity observed in the inverted models. The mineralogical phase transformation from spinel to garnet is considered as the origin of this discontinuity. The shallow depth of the discontinuity indicates an increase in upper mantle temperature which conforms to the high geothermal gradient reported in the region. The variation of depth of the discontinuity can be interpreted in terms of the addition of Cr+3 that shifts the spinel-garnet stability field to higher depths whereas Fe+2 shifts it to lower depths. Despite the high temperature in the upper mantle, the observed low Vp/Vs ratio (1.65–1.75) below the Hales discontinuity can be explained by the presence of a high fraction of orthopyroxene.