Introduction Streptococcus intermedius is part of the normal flora of the human mouth, but has a potential to invade the circulation resulting life-threatening infection. We report a case of S. intermedius infection of the left submandibular lymph node which was complicated by severe deep neck infection, in an immunocompetent child without any preceding risk factors. Case report A 16-month-old girl visited Chungnam National University Hospital for neck swelling. From 6 days before admission, the left side of her neck was swollen with mild fever of 38°C. No specific findings were seen in the past history including any dental care or trauma. About 10 cm sized mass-like lesion of the left submandibular area was firmly palpable, accompanied by mild heating sense and tenderness. Laboratory tests were as follows: white blood cell count 26,700 /μL, (segment neutrophil 66.7 %, lymphocyte 25.6 %), hemoglobin 10.1 g/dL, platelet 974,000 /μL, C-reactive protein 12.4 mg/dL, and lactate dehydrogenase 607 IU/L. Her immunoglobulin levels (IgG 1,217 mg/dL, IgA 156 mg/dL, IgM 193 mg/dL, and IgE 6.38 mg/dL) and T-cell subsets (T3 73.1%, T4 52.0%, T8 19.8%, and T4/T8 ratio 2.6) were all in normal range. Neck computed tomography showed an abscess (4.5 x 4.0 cm) in left parapharyngeal and submandibular spaces with right side deviation of central airway. After quinsy tonsillectomy, immediate surgical drainage of the abscess was successfully done via peroral approach without transcervical exploration or tracheotomy. Along with drainage, ampicillin/sulbactam antibiotic treatment was given. Cultures of abscess identified Streptococcus intermedius, sensitive to penicillin. After two weeks of antibiotic therapy, she completely recovered without complications. Conclusion Often presence of viridans streptococci in cultures are discounted as contaminant, our findings suggest that S. intermedius should be suspected in deep neck infections and pediatricians should be aware of the importance of this pathogen.