The maximal rate of heart rate (HR) increase (rHRI), a marker of HR acceleration during transition from rest to submaximal exercise, correlates with exercise performance. In this cohort study, whether rHRI tracked performance better when evaluated over shorter time-periods which include a greater proportion of HR acceleration and less steady-state HR was evaluated. rHRI and five-km treadmill running time-trial performance (5TTT) were assessed in 15 runners following one week of light training (LT), two weeks of heavy training (HT) and 10-day taper (T). rHRI was the first derivative maximum of a sigmoidal curve fit to one, two, three and four minutes of R-R data during transition from rest to running at 8 km/h (rHRI8 km/h), 10.5 km/h, 13 km/h and transition from 8 to 13 km/h (rHRI8-13km/h). 5TTT time increased from LT to HT (effect size [ES] 1.0, p < 0.001) then decreased from HT to T (ES -1.7, p < 0.001). 5TTT time was inversely related to rHRI8 km/h assessed over two (B = -5.54, p = 0.04) three (B = -5.34, p = 0.04) and four (B = -5.37, p = 0.04) minutes, and rHRI8-13km/h over one (B = -11.62, p = 0.006) and three (B = -11.44, p = 0.03) minutes. 5TTT correlated most consistently with rHRI8 km/h. rHRI8 km/h assessed over two to four minutes may be suitable for evaluating athlete responses to training.