Introduction: Stress fractures are injuries produced by the overuse of certain extremities, generating repetitive fatigue in the bone with insufficient rest periods and hormonal disorders, among others. High osteoclastic activity and lower activity of the osteoblasts at the cortical level occurs. Objective: To determine the factors associated with a stress fracture in a single medical center of the Peruvian navy. Methods: We conducted an observational, analytical case-control study. The dependent variable was stress fracture confirmed by magnetic resonance imaging of the patients; the independent variables were age, sex, calcemia, socioeconomic status, and time of daily physical activity. All data were extracted from the medical records. Crude and adjusted odds ratios were calculated with 95% confidence intervals. Results: The sample was comprised of 238 patients (119 cases and 119 controls), of which 79.8% were male, and 20.2% were female; the average age was 20.25. In the bivariate analysis, stress fractures were associated with male sex (odds ratio 3.00; 95% confidence interval 1.51 to 5.95), hypocalcemia (2.83; 2.32 to 3.44), more than two hours of daily physical activity (24.7; 12.51 to 48.95) and socioeconomic level C (6.66; 2.82 to 15.74). Time dedicated to physical activity (adjusted odds ratio 44.46; 95% confidence interval 17.93 to 110.22) and socioeconomic level C (adjusted odds ratio 22.57; 95% confidence interval 7.03 to 72.74) were associated in the multivariate analysis. Conclusion: We found that stress fractures were associated with physical activity time and a lower socioeconomic level. Further studies are needed to evaluate the relationship with other factors in the military population of Peru.