Premature ejaculation (PE) is one of the most common sexual disorders in men. Excessive activity of the sympathetic nervous system is considered as one of the pathological mechanisms of PE. Heart rate recovery (HRR) is a noninvasive and easily applicable method for evaluating autonomic functions. We aimed to investigate the relationship between PE and HRR. This cross-sectional study included 42 consecutive patients with lifelong PE and 98 healthy volunteers. All participants underwent stress tests according to age-dependent target heart rates outlined in the Bruce protocol. When the maximal heart rate was reached in the stress test, intensive exercise was terminated and electrocardiographic records were obtained for 3 min in the cool-down period. The HRR indices were calculated by subtracting the heart rate at first, second and third minutes from the maximal HR. The two groups were similar in terms of age, body mass index, serum glucose and lipid parameters. HRR indices were significantly lower in the PE group compared with the control group (p < .05 for all). Common factors that affect equilibrium of sympathetic and parasympathetic nervous systems may be involved in the PE and abnormal HRR etiopathogenesis. The cause-and-effect relationship can be more clearly demonstrated with large-scale, prospective studies.