The early Miocene unconformity (EMU) occurred during a transition in the tectonic evolution of western North America that impacted faunal diversification. The Railroad Canyon section in the northern Rocky Mountains provides a complete geologic record spanning this period. Our new magnetostratigraphic study in combination with published U-Pb ages from intercalated ash places the end of the EMU at ~20.1 Ma with a duration up to 1.5 Myr. The EMU is marked by an abrupt change in rock color, increase in magnetite concentration, and decrease in calcite abundance. The sudden changes in mineralogy reflect a reorganization in sediment source. Curiously, sedimentation rate remains constant at 6.5±0.1 cm/kyr through the EMU, as do climate proxies. Active uplift as well as drainage network reorganization seemingly contributed to EMU formation, possibly related to a change in tectonic regime such as the arrival of the Yellowstone plume and/or the onset of Basin and Range extension.