Introduction: Lemierre’s syndrome (LS) is a rare and serious condition that often affects school-aged children, adolescents, and healthy young adults. It is defined as an oropharyngeal infection with secondary septicemia, internal jugular vein thrombosis, and septic emboli. Rare cases of atypical LS in which thrombosis occurs in other locations have been reported. Case Presentation: We presented a case of an adolescent with fever, sore throat, and neck tenderness. Physical examination revealed acute pharyngitis and bilateral small cervical lymph nodes. Rapid antigen group A Streptococcus and viral serologic tests were negative. Complete hemogram and blood biochemical analysis showed leukocytosis and elevated serum C-reactive protein (CRP). Cervical computerized tomography (CT) scan revealed a heterogeneous right tonsil and small cervical lymph nodes. The chest radiograph was normal. After admission, the adolescent started complaining of dyspnea and thoracic pain and had a painful small cervical right mass. In the thoracic CT angiography (CTA), several pulmonary septic emboli were apparent throughout the pulmonary parenchyma. Cervical Doppler ultrasound showed right facial vein thrombophlebitis, later confirmed in a CTA. Thromboses in other locations, including the internal jugular vein, were excluded, as well as cervical abscesses. The patient was successfully treated with intravenous antibiotic therapy and anticoagulation. Discussion: To this date, no reports of LS presenting with isolated thrombosis of the facial vein have been described in pediatric patients. We highlighted the importance of early recognition of LS and its atypical variants. Pediatric international guidelines regarding its management and treatment would also greatly affect the outcome of these patients.