The Batrachosauroididae are an enigmatic group of salamanders known from the Cretaceous and Tertiary of North America and Europe. In Europe, the family is known only by two species of the genus Palaeoproteus. The genus has limited distribution in Western and Central Europe. In the present paper, we describe a new species, Palaeoproteus miocenicus, from the early late Miocene (11-9 Ma) of Austria and Ukraine, representing the youngest record of the family Batrachosauroididae from the Neogene of Europe. The new species differs from the Paleogene representatives of the genus by 12 characters, including large body size, the long anterior extension of the Meckelian groove and the size and shape of the odontoid process on the dentary. The µCT scanning of bones of the new species revealed novel features (e.g. anterior extension of Meckelian groove, interconnected network of canals and small cavities in atlas) observable only in this species. P. miocenicus inhabited aquatic environments, which existed under wet climatic conditions with mean annual precipitation higher than 900 mm. The new species expands the temporal range of the genus by at least 30 million years and enlarges the palaeogeographic distribution of the genus into Eastern Europe.