The Omura's whale (Balaenoptera omurai), previously referred to as a small form of Bryde's whale, was described in 2003 as a distinct baleen whale species of the family Balaenopteridae. Omura's whales are currently confirmed to occur in three of the world's oceans; the western Pacific, Indian, and northeastern Atlantic. Here we report the genetic identification and a morphological description of a 4.16 m female calf of an Omura's whale found stranded in Pecém beach (03°32′11.6″S, 38°47′51.8″W), northeastern Brazil, in 2010. The three mitochondrial DNA markers (control region, cytochrome b, and cytochrome c oxidase subunit 1) unequivocally identified the specimen as a B. omurai, providing the first report of this species in the South Atlantic Ocean. The morphological identification of the specimen was limited due to the absence of the skull and loss of color pattern, but the proportions of the body were not consistent with the other balenopterid species and a single rostrum ridge distinguished it from Bryde's whales. This, together with the record of another juvenile in Mauritania, suggests the existence of an autochthonous Atlantic population of Omura's whales and indicates a necessity of reassessment of specimens indicated as Bryde's whale in the region.