The Isanacetus-group is one of the most enigmatic groups of cetaceans. Although their phylogeny is still controversial, many previous studies suggested that they are a paraphyletic group of baleen whales, including an ancestor of Balaenopteridae and Eschrichtiidae. A new fossil from an Isanacetus-group baleen whale has been recovered from the Minamishirado Formation (latest early Miocene, Burdigalian), Iwaki, Fukushima Prefecture, Japan. The specimen consists of a cranium, mandible, and postcranial elements, including cervical, thoracic, and lumbar vertebrae, scapula, ulna, and ribs. We describe and diagnose the specimen as a new genus and species, Jobancetus pacificus. A unique combination of morphological characters characterized the specimen, e.g. frontals forming a triangular elevated plateau at the vertex, sharp, and well-developed transverse crest on the supraorbital process of frontal, sagittal crest formed by frontals and parietals, and large squamosal fossa, which is posteriorly extended well beyond the level of the posterior surface of the occipital condyle. Phylogenetic analysis under equal weighting suggests that J. pacificus is a stem group of Pligogulae, whereas the phylogenetic analyses under implied weightings suggest that J. pacificus is a stem group of Balaenopteridae + Eschrichtiidae. The discovery of J. pacificus expands our knowledge of the enigmatic Isanacetus-group.