Two specimens of fossil lipotid have been recovered from the Upper Miocene of Gunma and Tochigi prefectures, Japan. The specimens consist of crania including periotic and tympanic bullae. We describe and diagnose the specimens as a new genus and species of the family Lipotidae, Eolipotes japonicus, gen. et sp. nov. The paratype of E. japonicus, GMNH-PV-1011, was found stratigraphically between two tuff layers and a well constrained age interval (11.29–11.25 Ma) can be proposed, indicating that E. japonicus is the oldest precisely dated lipotid species yet described. Phylogenetic analysis revealed that E. japonicus is more closely related to Parapontoporia spp. than to the recently extinct Yangtze river dolphin, Lipotes vexillifer. Given the phylogenetic relationships and parsimonious distribution of the event to fluvial invasion in Lipotidae, it is suggested that at least two independent invasions to the freshwater habitat occurred in Lipotidae.