The study investigated the heart rate (HR) and heart rate variability (HRV) before, during, and after stretching exercises performed by subjects with low flexibility levels. Ten men (age: 23 ± 2 years; weight: 82 ± 13 kg; height: 177 ± 5 cm; sit-and-reach: 23 ± 4 cm) had the HR and HRV assessed during 30 minutes at rest, during 3 stretching exercises for the trunk and hamstrings (3 sets of 30 seconds at maximum range of motion), and after 30 minutes postexercise. The HRV was analyzed in the time ('SD of normal NN intervals' [SDNN], 'root mean of the squared sum of successive differences' [RMSSD], 'number of pairs of adjacent RR intervals differing by >50 milliseconds divided by the total of all RR intervals' [PNN50]) and frequency domains ('low-frequency component' [LF], 'high-frequency component' [HF], LF/HF ratio). The HR and SDNN increased during exercise (p < 0.03) and decreased in the postexercise period (p = 0.02). The RMSSD decreased during stretching (p = 0.03) and increased along recovery (p = 0.03). At the end of recovery, HR was lower (p = 0.01), SDNN was higher (p = 0.02), and PNN50 was similar (p = 0.42) to pre-exercise values. The LF increased (p = 0.02) and HF decreased (p = 0.01) while stretching, but after recovery, their values were similar to pre-exercise (p = 0.09 and p = 0.3, respectively). The LF/HF ratio increased during exercise (p = 0.02) and declined during recovery (p = 0.02), albeit remaining higher than at rest (p = 0.03). In conclusion, the parasympathetic activity rapidly increased after stretching, whereas the sympathetic activity increased during exercise and had a slower postexercise reduction. Stretching sessions including multiple exercises and sets acutely changed the sympathovagal balance in subjects with low flexibility, especially enhancing the postexercise vagal modulation.