The aim of this study was to determine urban–rural and regional differences in anthropometric characteristics among adolescents aged 12–14, as well as to present the prevalence of weight status. A total of 534 adolescents aged 12–14 from primary schools across Montenegro participated in this cross-sectional study (283 boys, aged 13.52 ± 0.42, body height 169.43 ± 8.89, body weight 60.54 ± 13.47; 251 girls, aged 13.51 ± 0.40, body height 165.54 ± 6.67, body weight 55.28 ± 9.27). The sample was divided by geographic region in Montenegro into northern, central, and coastal regions, and according to settlement type into urban and rural inhabitants. Anthropometric characteristics were assessed using a battery of seven variables: arm span (AS); body height (BH); body weight (BW); waist circumference (WC); hip circumference (HC); body mass index (BMI); and waist-to-hip ratio (WHR). BMI was categorized based on the World Health Organization’s (WHO) cut-offs. The results indicate that girls from urban areas exhibited significantly greater body height and lower BMI values compared to their rural counterparts. Similarly, boys from urban areas also demonstrated lower BMI values compared to their rural peers. However, no statistically significant differences were observed in other anthropometric characteristics between these two groups of adolescents. Based on analysis of variance (ANOVA) and post-hoc analysis, it was found that girls from central areas had significantly greater body height compared to those from northern and coastal areas. Likewise, boys from northern areas showed higher body mass and BMI values compared to those from central areas. Additionally, both boys and girls from central areas had higher values compared to those from coastal areas. Nevertheless, no significant differences were detected in other anthropometric characteristics among adolescents from these regions. This study identified significant differences in anthropometric parameters among participants based on urban–rural status and within regional divisions. However, further research encompassing a larger sub-sample and a broader array of anthropometric variables is needed to draw a more comprehensive conclusion.