A 25-year-old man with no underlying diseases presented to a local physician because of fever. He was diagnosed by rapid diagnostic test as having type B influenza virus infection. The fever did not resolve, and chest X-ray revealed infiltrative shadows; so he was referred to our hospital on the 4th day after presentation. Computed tomography findings showed bilateral multiple nodules, suggesting septic embolization, and he was admitted. Fusobacterium necrophorum was cultured from a blood specimen, and the diagnosis was established. Although empyema combined with fistula developed, the patient improved with antibiotics and chest drainage. F. necrophorum is the most common pathogen isolated in patients with Lemierre syndrome. Venous thrombosis was not present in our patient, so we surmised that the F. necrophorum-related sepsis occurred during pharyngitis of influenza infection. In patients who develop septic pulmonary embolism after influenza virus infection, F. necrophorum should be considered as a possible pathogen.