Orexin maintains wakefulness through the orexin receptor 2 (OX2R), and dysfunction of OX2R results in the fragmentation of wakefulness and the cataplexy-like behavioral arrest which is similar to narcolepsy. Orexin also contributes to emotional stress and other state-dependent related regulation of ventilation, e.g., the defense response. On the other hand, the parabrachial nucleus (PBN), which is known as a pontine respiratory modulating center, is considered as an inspiratory termination and chemoreception. We reported previously the PBN plays an active inspiratory-expiratory phase switching in neonatal rat. However, the effects of orexin on the relationship between respiration and chemoreception in neonatal stage of the pons had not been investigated. In this study, we examined the distribution of orexinergic axon fibers in the PBN of neonatal rat and the effects of orexin on respiration and respiratory PBN neurons under hypercapnic and hypoxic conditions. According to immunohistological study for orexin, orexin-immunoreactive axon fibers were observed in the PBN even at P0, and the numbers of them at P5 were as much as those at adulthood. In the neonatal rat brainstem-spinal cord preparation, the firing rate of inspiratory-expiratory phase-switching neuron (I-E neuron), which fires from late inspiratory to early expiratory phase, was increased by superfusion of orexin B. Under the hypercapnia and hypoxia, orexin B caused higher respiratory rate and the firing rate of I-E neurons located in the PBN. Compared to hypoxia, more frequent burst activities in one respiratory phase appeared in hypercapnia. Orexin B increases respiratory rate by facilitating I-E neuron activity in the PBN using inspiratory termination as an active phase-switching, and hypercapnia is more important for controlling respiratory rate by orexin than hypoxia. The elucidation of orexin neurotransmitter system would lead to understanding of what regulates sleep-wakefulness stage, and to novel therapeutic advances for emotional stress.