The purpose of this study was to investigate whether a treadmill endurance exercise program would reduce serum testosterone and leptin in male rats and assess the impact of increased dietary cholesterol on serum hormones. Male Sprague-Dawley Rats (n = 20) were randomly assigned to a control group (C) or an exercise training group (EX) that performed treadmill running 40 min/day, 6 days/week for 12 weeks. At study midpoint (week 6), rats were randomized to a high-cholesterol (HC) diet (n = 10) or remain on standard semi-purified (LC) diet (n = 10). Results are presented as median [IQR]. At end of week 6, EX + LC had significantly lower body weight (508 [460–527] vs 570 [516–606] g; p = 0.01), mean daily energy intake (76.3 [74.9–82.2] vs 90.9 [86.9–94.5] kcal; p < 0.01), and serum leptin (0.4 [0.3–0.6] vs 3.3 [2.0–4.0] ng/mL; p < 0.01) in comparison to C + LC. No difference was observed between EX + LC and C + LC in serum testosterone (12.6 [6.9–18.3] vs 11.7 [7.6–18.9] ng/mL). At end of week 12, EX + LC had significantly lower body weight (514 [483–568] g) compared to C + LC (644 [575–680] g; p < 0.01) and C + HC (650 [583–702] g; p < 0.01). Serum Leptin in both EX + LC (0.6 [0.2–0.8] ng/mL) and EX + HC (0.6 [0.3–1.6] ng/mL) was significantly lower than C + LC (3.0 [2.2–4.2] ng/mL; p < 0.01). No significant difference in testosterone was observed between C + LC and C + HC (4.3 [3.3–8.3] vs 6.3 [3.2–9.3] ng/mL, respectively). Despite lower energy availability, exercise-induced changes in sex hormones may not occur in training programs ≤ 12 weeks. Lower voluntary energy intake observed in exercise groups despite greater energy expenditure may indicate that lower energy availability in endurance-trained individuals may be inadvertent.