Physical activity is central in prevention and treatment of metabolic syndrome. High‐intensity aerobic exercise can induce larger energy expenditure per unit of time compared with moderate‐intensity exercise. Furthermore, it may induce larger energy expenditure at post‐exercise recovery. The aim of this study is to compare the excess post‐exercise oxygen consumption (EPOC) in three different aerobic exercise sessions in men with metabolic syndrome. Seven men (age: 56.7 ± 10.8) with metabolic syndrome participated in this crossover study. The sessions consisted of one aerobic interval (1‐AIT), four aerobic intervals (4‐AIT), and 47‐min continuous moderate exercise (CME) on separate days, with at least 48 h between each test day. Resting metabolic rate (RMR) was measured pre‐exercise and used as baseline value. EPOC was measured until baseline metabolic rate was re‐established. An increase in O2 uptake lasting for 70.4 ± 24.8 min (4‐AIT), 35.9 ± 17.3 min (1‐AIT), and 45.6 ± 17.3 min (CME) was observed. EPOC were 2.9 ± 1.7 L O2 (4‐AIT), 1.3 ± 1.1 L O2 (1‐AIT), and 1.4 ± 1.1 L O2 (CME). There were significant differences (P < 0.001) between 4‐AIT, CME, and 1‐AIT. Total EPOC was highest after 4‐AIT. These data suggest that exercise intensity has a significant positive effect on EPOC in men with metabolic syndrome.