Lemierre’s syndrome (LS) is a rare clinical condition characterized by septic thrombophlebitis of the internal or external jugular vein, usually following an oropharyngeal infection. Here, we present a 20-year-old male patient who developed diarrhea, nausea, and vomiting after receiving clarithromycin for an upper respiratory tract infection. On admission, he had fever, hypotension, and elevation in acute phase reactants (WBC: 20,410/µL, CRP: 197 mg/L). Empirical treatment with ceftriaxone and metronidazole was initiated. Stool and throat cultures were negative. On the second day, abdominal tenderness developed; direct abdominal radiograph showed dilated bowel loops, but toxic megacolon was excluded during follow-up. Thoracic CT revealed septic emboli in the lungs. Due to persistent fever despite ceftriaxone and metronidazole therapy, treatment was escalated to meropenem on the fifth day. On the same day, blood cultures grew Fusobacterium necrophorum, raising suspicion of LS. Doppler ultrasound detected a thrombus in the left external jugular vein. Anticoagulant therapy with low-molecular-weight heparin and clopidogrel was initiated. The fever resolved by the seventh day of full antibiotherapy After three weeks of intravenous therapy, follow-up imaging showed regression of the thrombus. The patient completed a four-week course of antibiotics and anticoagulants and was discharged with full recovery. This case highlights the diagnostic challenge of LS presenting with gastrointestinal symptoms and emphasizes the importance of early blood cultures and imaging. External jugular vein involvement due to F. necrophorum is rare and should be considered in patients presenting with septic emboli.