Examining the trend of anthropometric indices in children and adolescents in each region can be highly beneficial in providing effective strategies to improve the status of their growth. This study was conducted with the aim of determining the trend of anthropometric indices in students from primary to high school in the west of Iran. Data were collected using a demographic questionnaire and health certificates for anthropometric information of primary school students, and current anthropometric measurements with scale for high school students. Then, all of the data were analyzed in AnthroPlus and SPSS software. Of the 731 students, 350 were female and 381 were male. Mean height Z-score to age showed a significant reduction from primary to high school (from +0.0386 to −0.27416), and mean body mass index Z-score to age showed a significant increase (from −0.3916 to +0.1826). Prevalence of stunting and overweight/obesity in high school was 1.4 and 2.5 times higher than primary school, respectively, but the prevalence of wasting reduced by 2.3 fold. Girls were more affected by the increased trend of obesity and stunting compared to boys. Nutritional transition was evident in students. Healthcare policy-makers should design and implement a comprehensive health strategy to deal with this situation, especially in girls.