Lateral neck masses (LNM) often present a diagnostic challenge in the practice of pediatric plastic surgeon. The aim of this study is to investigate the clinical and ultrasound (US) characteristics of pediatric LNM in order to make mutual comparison between their entities and enable the most accurate preoperative diagnosis. A cross-sectional study was conducted among 250 pediatric patients treated by surgical excision or sclerotherapy in our institution in the period from July 2009 to June 2019. Lymphatic malformation was the most frequent congenital LNM (60.9%), while reactive or granulomatous lymphadenitis was the most frequent acquired LNM (47%). Congenital anomalies were significantly more often localized in the upper half of the sternocleidomastoid (SCM) muscle region, and had more often soft consistency than acquired ones. Congenital LNM had a 32.37 (3.44–304.63) times higher likelihood of incorrect (p = 0.002) and 5.86 (1.35–25.48) times higher likelihood of undetermined (p = 0.018) than correct US findings, respectively. Acquired LNM were significantly more often localized in the region behind the SCM muscle and more often had solid US appearance in comparison to the congenital ones. Association of the clinical and US findings is very important in determining the most accurate preoperative diagnosis without exposing the children to unnecessary utilizing ionizing radiation or anesthesia. Although they are mostly benign, extreme caution is necessary due to malignancies which were found in 16.4% of all our patients.