The cycling wheelchair (CWC) can be used as a pedaling exercise machine. However, physiological indexes in the CWC at various pedaling rates and the difference between the CWC and the existing pedaling machines such as the portable ergometer (ERG) are unclear. The aim of this study was to measure physiological indexes in the CWC at various pedaling rates and compare the CWC to the ERG, focusing on psychological stress. The present non-randomized crossover study included ten healthy men (22.3 ± 1.2 years) who performed pedaling exercise with the CWC and the ERG. Both experiments were composed of three pedaling exercise sessions (40, 60, and 80 rpm). Physiological indexes, consisting of oxygen consumption, heart rate, perceived breathlessness and leg fatigue, and salivary amylase activity (SAA), an index of psychological stress, were measured. The metabolic equivalent (METs) and the rate of change in SAA from rest to immediately after each pedaling session (ΔSAA) were calculated. In the CWC, all physiological indexes significantly increased with pedaling rates. The METs were 2.2 ± 0.3, 2.7 ± 0.4, and 3.5 ± 0.4 at 40, 60, and 80 rpm, respectively. In comparison between the CWC and the ERG, ΔSAA was lower in the CWC than in the ERG at 60 and 80 rpm. Our results indicate that the CWC pedaling can provide low or moderate intensity exercises with adjusting pedaling rates and is less stressful than the ERG. Thus, the CWC is a useful pedaling machine to promote regular and enjoyable exercises.