We describe a case of systemic toxoplasmosis in a female adult narrow-ridged finless porpoise (Neophocaena asiaeorientalis) found in May 2018 inside a gillnet set in the Ariake Sound, southern Japan. The main lesions observed were lymphoplasmacytic and focally necrotizing encephalitis, necrotizing to granulomatous adrenalitis, myocarditis, and inflammation in the intestinal wall, associated with protozoal tissue cysts and tachyzoites. Additionally, the individual had a 5.6 mm (crown-rump length) early-stage embryo in the left uterine horn, which had multifocal necrotizing lesions with intralesional tissue cysts and tachyzoites in the parenchyma. Immunohistochemistry and PCR and sequencing of the internal transcribed spacer 1 region confirmed a Toxoplasma gondii infection. Further genotyping revealed an atypical type II genotype with a type I pattern for the Apico locus. Narrow-ridged finless porpoises are an endangered coastal species already facing various anthropogenic threats. Toxoplasmosis, especially with its ability to transmit to an early-stage embryo, should be considered an emerging threat to this vulnerable species.