The aim of this paper was to explore the influence of the epicardial fat (EF) tissue on heart rate recovery (marker of autonomic dysfunction) and cardiorespiratory fitness in middle-aged men. This cross-sectional study was performed on 101 overweight or obese men. The results showed that higher EF thickness was associated with lower heart rate recovery at 1 and 2 minutes, a representation of autonomic dysfunction. Accordingly, EF tissue was negatively associated with cardiorespiratory fitness in men, independent of body weight. These data suggest that the presence of higher EF thickness in obese men may have a negative impact on cardiorespiratory fitness and autonomic dysfunction during exercise testing compared to men with low EF levels.