Although previous studies have investigated the effect of hyperventilation induced respiratory alkalosis on oxygen uptake kinetics during exercise for the transition on oxygen uptake, the mechanism is still unclear. This study aimed to investigate the effect of a controlled respiratory rate on oxygen uptake kinetics during cycling exercise. Five healthy men participated in this study. The subjects performed baseline cycling exercise for 4 min at 10 W, followed by primary cycling exercise for 6 min at anaerobic threshold (AT), AT minus 40% of the difference between AT and the peak pulmonary oxygen uptake (AT − Δ40%), or AT + Δ40% intensities. Throughout the experiment, respiratory rate of each subject was maintained at 20, 30, or 60 breaths/min (bpm). The pulmonary gas exchange was measured breath by breath, the heart rate was measured using a cardiogram, and the oxy- and deoxyhemoglobin concentrations of the vastus lateralis muscles were estimated using near-infrared spectroscopy at 1 Hz. The kinetics analysis was conducted by using the oxygen uptake response curves and deoxyhemoglobin concentrations during transition to primary exercise. A one-way analysis of variance was used for comparing kinetic values among respiratory rates or workloads. When a significant difference was detected, the post-hoc Scheffe’s test was used to identify significant differences. As the respiratory rate was high, the end-tidal partial pressure of CO2 was lower (20 bpm: 32.7 ± 3.2 mmHg, 30 bpm: 31.1 ± 1.8 mmHg, 60 bpm: 21.7 ± 2.1 mmHg) during baseline exercise. Similarly, as the respiratory rate was high in the analysis of oxygen uptake kinetics, the time delay significantly increased (20 bpm: 12.8 ± 2.4 s, 30 bpm: 15.4 ± 2.1 s, 60 bpm: 18.9 ± 4.2 s in AT + Δ40%; P < 0.05) and time constant significantly decreased (20 bpm: 52.2 ± 10.4 s, 30 bpm: 36.2 ± 8.4 s, 60 bpm: 27.9 ± 8.9 s in AT + Δ40%; P < 0.05). The time delay and time constant did not differ significantly according to the workload. Similarly, active muscle deoxygenation did not differ significantly according to the respiratory rate and workload. Increase in the time delay at higher respiratory rates suggest that the ATP was mainly supplied by anaerobic metabolism, because the oxyhemoglobin dissociation curve shifted to the left owing to respiratory alkalosis. Decrease in the time constant after an increase in the time delay at higher respiratory rates suggest that the oxyhemoglobin dissociation curve shifted to the right owing to acidification; this occurred because compensation of respiratory alkalosis caused a decrease in the [HCO3−] and anaerobic metabolism increased the lactic acid concentration.