Non-tuberculous mycobacteria are one of the major causes of lymphadenitis in children and seldom of deep neck infections. We reported the case of an immunocompetent two-year-old girl with adenitis and retropharyngeal abscess caused by an atypical mycobacterium. She had a positive tuberculin skin test, whereas the Quantiferon TB Gold test was negative. The child underwent a complete nodal excision. The search for acid fast bacilli was positive and Mycobacterium scrofulaceum was isolated from the surgically removed material. The retropharyngeal abscess was treated only with antimicrobial therapy, which resulted in an appreciable size reduction of the abscess. After two months antimicrobial treatment was interrupted, and complete resolution was achieved after twelve months. No relapse of disease or possible long-term complications were observed. The surgical wound healed completely, with normal overlying skin and a good aesthetic result. The clinical management of atypical mycobacteria lymphadenitis and retropharyngeal abscess in children is discussed.