We examined whether the system analysis for step and pseudorandom binary sequence (PRBS) exercises could be useful to characterize oxygen uptake (VO2) kinetics of female sedentary subjects and endurance athletes. Breath-by-breath VO2 was determined during step- and PRBS-cycle ergometer exercises. The time course of the VO2 kinetics was evaluated by the time constant of the second phase, which should reflect the adjustment of the oxidative metabolism at the skeletal muscle level. The VO2 kinetics were significantly faster in long-distance runners than in sedentary subjects for both exercises. A significant relationship was observed in the VO2 kinetics obtained from step and PRBS exercises. In each group, there was no significant difference in the VO2 kinetics for step and PRBS exercises. These results indicated that the system analysis with PRBS exercises revealed the faster VO2 kinetics in endurance athletes than in sedentary subjects.