Bilophila wadsworthia is a Gram-negative anaerobic bacterium. In current study, it was identified in the bloodstream of a 69-year-old man admitted to the Neurology Clinic at the University of Debrecen, Clinical Centre, Hungary, for internal carotid artery stent implantation. Bacteraemia caused by B. wadsworthia is extremely rare, with very few cases reported worldwide. This case is notable because it is the first instance in which whole-genome sequencing of B. wadsworthia derived from blood was performed. Moreover, the sequence data have been deposited in a public database.