Purpose: Cardiometabolic risk factors can originate in childhood, especially in overweight individuals. In this study, we aimed to determine the trends in the prevalence of metabolic phenotypes among Iranian children and adolescents. Methods: We determined the trends of the data from 3 nationwide school-based studies in Iran from 2003 to 2016 (the CASPIAN [Childhood and Adolescence Surveillance and Prevention of Adult Non-communicable Disease] studies). A total of 8,711 individuals (49.6% boys) aged 10–18 years were studied. Obesity and normal weight were considered as an age- and sex-specific body mass index > 95th percentile and between the 5th to 85th percentile, respectively. Metabolic syndrome (MetS) was defined according to the modified Adult Treatment Panel III criteria for children and adolescents. Children were categorized into 4 groups: metabolically healthy obesity (MHO), metabolically unhealthy obesity (MUO), metabolically healthy normal weight, and metabolically unhealthy normal weight (MUNW). Results: Over 13 years, the prevalence of obesity increased significantly from 9.8% to 11.6% (p<0.001), whereas that of MetS did not change significantly (from 5.35% in 2003–2004 to 7.76% in 2009–2010 and 4.45% in 2015-2016, p=0.83). The prevalence of MHO increased significantly from 7.1% in 2004 to 9.6% in 2016 (p=0.005). However, the change in prevalence was not significant for MUO and MUNW. Conclusion From 2003 to 2016, the prevalence of MetS and metabolic phenotypes except MHO did not change significantly among Iranian children. The marginal increase in MHO prevalence should be considered, as shifts from this phenotype to unhealthy phenotypes may influence the risk of developing noncommunicable diseases in adulthood.