The aim of this work was to investigate the time and exercise intensity dependence of heart rate variability (HRV). Time-dependent, cardiovascular-drift-related increases in heart rate (HR) were inhibited by enforcing a constant heart rate throughout the exercise with a feedback control system. Thirty-two healthy adults performed HR-stabilised treadmill running exercise at two distinct exercise intensity levels. Standard time and frequency domain HRV metrics were computed and served as outcomes. Significant decreases were detected in 8 of the 14 outcomes for the time dependence analysis and in 6 of the 7 outcomes for the exercise intensity dependence analysis (excluding the experimental speed-signal frequency analysis). Furthermore, metrics that have been reported to reach an intensity-dependent near-zero minimum rapidly (usually at moderate intensity) were found to be near constant over time and only barely decreased with intensity. Taken together, these results highlight that HRV generally decreases with time and with exercise intensity. The intensity-related reductions were found to be greater in value and significance compared to the time-related reductions. Additionally, the results indicate that decreases in HRV metrics with time or exercise intensity are only detectable as long as their metric-specific near-zero minimum has not yet been reached.