The Cenozoic strata of the Xining Basin, NE Tibet, have provided crucial records for understanding the tectonic and palaeo-environmental evolution of the region. Yet, the age of the lower part of the sedimentary stratigraphy and, consequently, the early tectonic evolution of the basin remain debated. Here, we present the litho- and magnetostratigraphy of various early Eocene sections throughout the Xining Basin independently constrained by the U–Pb radiometric age of a carbonate bed. Our study extends the dated stratigraphy down to 53.0 Ma (C24n.1r) and reveals highly variable accumulation rates during the early Eocene ranging from 0.5 to 8 cm/ka. This is in stark contrast to the low but stable accumulation rates (2–3 cm/ka) observed throughout the overlying Palaeogene and Neogene strata. Such a pattern of basin infill is not characteristic of flexural subsidence as previously proposed, but rather supports an extensional origin of the Xining Basin with multiple depocentres, which subsequently coalesced into a more stable and slowly subsiding basin. Whether this extension was related to the far-field effects of the subducting Pacific Plate or the India–Asia collision remains to be confirmed by future studies.