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Background Obesity is a known risk factor for hypertension, but the extent to which physical activity mediates this relationship remains unclear.Methods Cross-sectional data from medical exams of Swiss Armed Forces conscripts between 2007 and 2022 (N=382 583). Physical fitness was assessed via the Conscription Physical Test (CPT), which included five components, one of which was an endurance test (ET). Both CPT and ET results were categorised as ‘fit’ or ‘unfit’. Weight status was classified based on body mass index (BMI) into normal weight, overweight (BMI 25–29.99) and obesity (BMI≥30 kg/m²). Hypertension was defined as ≥140/90 mm Hg. The study explored CPT and ET as mediators between BMI and hypertension.Results 20.6% of the conscripts had hypertension, 20.4% overweight and 4.5% obese. Conscripts with overweight or obesity had a higher risk of hypertension compared with normal weight (OR and (bias-corrected 95% CI) of natural direct effect: 1.803 (1.766 to 1.845) and 2.727 (2.570 to 2.865)), with a protective effect of being fit (natural indirect effect for CPT: 0.976 (0.971 to 0.982) and 0.917 (0.881 to 0.953)). When ET was assessed, similar findings were obtained: 1.765 (1.731 to 1.804) and 2.680 (2.482 to 2.887) for overweight and obesity, with a protective effect of being fit (0.991 (0.983 to 0.999) and 0.925 (0.861 to 0.991)).Conclusions Male Swiss conscripts with overweight and obesity face an increasing risk of hypertension, with the protective benefit of physical fitness showing an increasing trend as BMI increases.