The present study proposes to measure and quantify the heart rate variability (HRV) changes during effort as a function of the heart rate and to test the capacity of the produced indices to predict cardiorespiratory fitness measures. Therefore, the beat-to-beat cardiac time interval series of 18 adolescent athletes (15.2 ± 2.0 years) measured during maximal graded effort test were detrended using a dynamical first-order differential equation model. HRV was then calculated as the standard deviation of the detrended RR intervals (SDRR) within successive windows of one minute. The variation of this measure of HRV during exercise is properly fitted by an exponential decrease of the heart rate: the SDRR is divided by 2 every increase of heart rate of 20 beats/min. The HR increase necessary to divide by 2 the HRV is linearly inversely correlated with the maximum oxygen consumption (r = -0.60, p = 0.006), the maximal aerobic power (r = -0.62, p = 0.006), and, to a lesser extent, to the power at the ventilatory thresholds (r = -0.53, p = 0.02 and r = -0.47, p = 0.05 for the first and second threshold). It indicates that the decrease of the HRV when the heart rate increases is faster among athletes with better fitness. This analysis, based only on cardiac measurements, provides a promising tool for the study of cardiac measurements generated by portable devices.