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Hyperleptinaemia is an emerging mechanism involved in the pathogenesis of obesity-related primary hypertension (HTN). This substudy from a large clinical trial aimed to determine differences in [leptin] in physically inactive adults (n = 69, 46.4% women) with HTN and living with overweight or obesity following a 16-week supervised aerobic exercise training (EX group, 2 days/week) intervention with an attention control (AC, only physical advice) group, both combined with a hypocaloric diet; to analyse whether the changes observed after the intervention were maintained after 6 months (6M); and to explore differences and potential mechanisms affected by sex. Cardiorespiratory fitness and body composition evaluation, and biochemical measurements were conducted. After the intervention [leptin] decreased in both groups (EX, 36%, p = 0.003; AC, 23%, p = 0.06), returning to baseline concentrations after 6M of follow-up in both groups. Changes over time were similar in both sexes, with no significant time × group interaction (p > 0.05). For all participants, body mass index was the only factor independently associated with [leptin] (β = 0.339, B = 2.11, SE = 0.53), explaining 12% of the variability (p < 0.001). Among women, waist-to-hip ratio (12%, β = 0.365, B = 135.8, SE = 59.4) and fat-free mass (11%, β = -0.443, B = -2.33, SE = -2.27) additionally and independently explained leptin variability (p < 0.05). A hypocaloric diet combined with supervised exercise appears to be an effective strategy for regulating [leptin] and improving metabolic health in individuals with HTN and overweight or obesity. The influence of fat distribution on leptin dynamics in women calls for research to consider sexual dimorphism.