We examined the hypothesis that delayed heart rate recovery (HRR) after exercise testing, an estimate of decreased autonomic function, predicts the risk of cardiometabolic syndrome (MetS) and is associated with continuous MetS risk scores in healthy men. Participants were 2,740 men who underwent general health examinations and had no evidence of MetS, cardiovascular diseases, diabetes, and hypertension at baseline. Baseline HRR was calculated as the difference between peak heart rate attained during exercise testing and the heart rate at 1 (HRR 1) and 2 minutes (HRR 2) after test termination. Incident MetS was defined as participants having ≥3 MetS components, and continuous MetS risk score was computed as the sum of z-score of 5 risk factors at follow-up. The incidence of MetS was 61/1,000 person-years during an average follow-up of 5 years. The relative risks and 95% confidence interval (CI) of incident MetS in the lowest quartiles of HRR 1 and HRR 2 versus the highest quartile were 1.24 (95% CI 1.02 to 1.51) and 2.02 (95% CI 1.58 to 2.60), respectively, after adjusting for potential confounders, including peak oxygen uptake and resting heart rate. HRR 1 (ß = −0.052, p = 0.005) and HRR 2 (ß = −0.058, p = 0.009) were independently associated with clustered MetS risk scores after adjusting for covariates. In conclusion, the independent association between delayed HRR after exercise testing and incident MetS and continuous MetS risk scores suggests that decreased autonomic function may be considered as a parameter to predict the future likelihood of MetS.