This study evaluated the nutritional status of Syrian refugees in the early adolescent period living in different vulnerable settings. Nutritional assessment of Syrian refugee adolescents is often neglected but essential for a healthy physical, pubertal and mental development. Growth parameters of Syrian refugee adolescents going to a public school in an urban area and in a temporary protection center (TPC) were recorded along with the Turkish adolescents. Stunting percentages were similar between the groups (p = 0.811). While the proportion of children with a BMI over 85th percentile were significantly higher among Syrian adolescents living in TPC, Turkish children have the highest percentage of underweight (p = 0.01). Both food insecurity and unhealthy weight gain continue to be major concerns for refugee adolescents after their resettlement to a host country. The findings suggest that nutritional assessment and intervention at early adolescence is critical for Syrian refugees depending on their living conditions.