The ventilatory response to moderate-intensity step load exercise has three temporal phases: an initial rapidly increasing phase I, followed by a slower exponential phase II, that leads to the steady state phase III. In muscles with mechanical hyperalgesia (delayed onset muscle soreness) and/or muscle damage a few days after eccentric exercise (ECC), an interesting phenomenon of increased ventilatory response at phases II and III during constant-load exercise and incremental exercise has been reported. However, the mechanisms behind this phenomenon have not been clarified. At least a neural mechanism is partly responsible for this phenomenon because the ventilatory response at neurally modulated phase I has been shown to be exaggerated 2 days after ECC (D2). In the present review, we focus on our previous work to identify the potential mechanism underlying the exaggerated modulation in phase I ventilatory response at D2, in which ECC-induced muscle pain is assumed to be at the peak. We also discuss the physiological and practical implications of this phenomenon.