It has been suggested that the increase in heart rate (HR) at the onset of exercise is caused by vagal withdrawal. In fact, endurance runners show a lower HR in maximum aerobic tests. However, it is still unknown whether endurance runners have a lower HR at 4 s after the onset of exercise (4th-sec-HR). We sought to measure the HR at the onset of the 4 s exercise test (4-sET), clarifying its relationship to heart rate variability (HRV), spectral indices, and cardiac vagal index (CVI) in endurance runners (ER) and healthy untrained controls (CON). HR at 4th-sec-HR, CVI, and percent HR increase during exercise were analyzed in the 4-sET. High frequency spectrum (HF-nu), low frequency spectrum (LF-nu), and low frequency/high frequency band ratio (LF/HF) were analyzed from the HRV. ER showed a significantly higher HF, and both a lower LF and LF/HF ratio compared with the CON. ER presented a significantly lower 4th-sec-HR, although neither CVI nor HR increases during exercise were statistically different from the CON. In conclusion, ER presented a lower 4th-sec-HR secondary to increased vagal influence over the sinus node. CVI seems to be too weak to use for discriminating individuals with respect to the magnitude of HR vagal control.