Abstract Background Although ultrasound is regarded as the first choice imaging modality for evaluating a pediatric neck mass, neck computed tomography (CT) is necessary for urgent surgical conditions such as deep neck infections. Our aim was to evaluate the diagnostic effectiveness of and proper patient selection for neck CT as a method for the initial evaluation of pediatric neck masses in the emergency department. Methods We analyzed the medical records of 105 pediatric patients who visited the emergency department with neck mass whose initial imaging work-up was a neck CT and who visited the emergency department with a neck mass. The parameters investigated included the patient’s age, sex, symptom duration, clinical impression, CT interpretation, final diagnosis, and treatment. The positive predictive value (PPV) for CT was calculated, and the parameters that correlated with an urgent surgical condition post-CT were evaluated. Results The median age was 6.5 years (1 month to 12 years), and the male-to-female ratio was 2:1. The most common initial impression was acute cervical lymphadenopathy. A comparison of the final diagnosis and CT scan demonstrated that the overall PPV was 96.2%. If the initial impression was a deep neck infection, a salivary gland infection, or tonsillitis, the PPV for CT was 100%. Fever (>38.0°C) and severe tenderness were significant between patients with and without urgent surgical conditions on CT. Conclusions Computed tomography could be considered as the first diagnostic modality when an urgent surgical condition such as a deep neck infection is highly suspected.