The aim of this study was to analyze the association between the practice of physical activity and health-related physical fitness in adolescents participating and not participating in a guided physical activity program in municipal schools in the city of Fortaleza. We investigated 755 adolescents of both sexes, 385 from the Second Time Program (PST) and 370 from the Control Group (CG), aged between 10 and 14, from municipal schools in the city of Fortaleza, CE. Body mass index (BMI), sexual maturation and health-related physical fitness were assessed, as well as sedentary behavior and eating habits. Girls were found to be superior in the sit and reach test and boys in the abdominal and cardiorespiratory endurance tests. It was found that 16.7% and 3.7% of the sample were overweight and obese, respectively. Consumption of unhealthy foods such as sweets (51.3%) and soft drinks (15.8%) were the highest in both sexes.