Low energy availability, defined as low caloric intake relative to exercise energy expenditure, has been linked to endocrine alterations frequently observed in chronically energy-deficient exercising women. Our goal was to determine the endocrine effects of low energy availability in exercising men. Six exercising men (VO_2peak: 49.3 ± 2.4 ml · kg⁻¹ · min⁻¹) underwent two conditions of low energy availability (15 kcal · kg⁻¹ fat-free mass [FFM] · day⁻¹) and two energy-balanced conditions (40 kcal · kg⁻¹ FFM · day⁻¹) in randomised order. During one low energy availability and one balanced condition, participants exercised to expend 15 kcal · kg⁻¹ FFM · day⁻¹; no exercise was conducted during the other two conditions. Metabolic hormones were assessed before and after each 4-day period. Following both low energy availability conditions, leptin (−53% to −56%) and insulin (−34% to −38%) were reduced (P < 0.05). Reductions in leptin and insulin were independent of whether low energy availability was attained with or without exercise (P > 0.80). Low energy availability did not significantly impact ghrelin, triiodothyronine, testosterone and IGF-1 (all P > 0.05). The observed reductions in leptin and insulin were in the same magnitude as changes previously reported in sedentary women. Further research is needed to understand why other metabolic hormones are more robust against low energy availability in exercising men than those in sedentary and exercising women.