This study aimed to automatically classify physical fitness and cardiometabolic risk in a Chilean adolescent using self-organizing maps. This cross-sectional study analysed a nationally representative database from the Physical Education Quality Measurement System (n = 7197). Physical fitness and cardiometabolic risk variables were derived from anthropometric indicators. Self-Organizing maps (SOM) were employed to identify participant profiles based on an unsupervised predictive model. After implementing and training the SOM, a detailed analysis of the generated maps was conducted to interpret the revealed relationships and clusters. The analysis resulted in three classification groups, categorizing the sample into low, moderate, and high-risk levels. Students with better physical fitness exhibited lower cardiometabolic risk levels and a lower body mass index. SOM, through an unsupervised model, is a reliable tool for classifying cardiometabolic risk and physical fitness in adolescents.