Today, the situation of Syrian refugees is one of the world’s worst humanitarian crises. To estimate the prevalence of malnutrition among pediatric populations of Syrian refugees, 176 Syrian refugee children, with stays of more than two years at three refugee camps (Zalhé, Deddeh, and Kfar Jouz) or from the town of Yohmor, Lebanon were authorized by their parents to participate in this study. The children were anthropometrically evaluated and height-for-age Z-score (HAZ), weight-for-age Z-score (WAZ), and weight-for-height (WHZ) Z-scores were obtained and compared with WHO standards. Furthermore, mid-upper arm circumference (MUAC) was analyzed for screening children 6–59 months old. According to the anthropometric measures, no child met the criteria for chronic, global, acute malnutrition (CGAM), severe acute malnutrition (SAM), or moderate acute malnutrition (MAM). In the total sample, 49.4% of participants were moderately thin, with girls presenting a higher prevalence of thinness than that of boys. Thus, the absence of high rates of malnutrition was verified despite the magnitude of the Syrian refugee’s problem. The data provided by this study identify the need to carry out further research to assess anthropometric growth and nutritional status among long-staying refugee children in order to prevent any health issues that may arise in the future.