Key points Central hypercapnic hypoventilation is highly prevalent in children suffering from congenital central hypoventilation syndrome (CCHS). Mutations of the gene for paired‐like homeobox 2b (Phox2b) are aetiologically associated with CCHS and Phox2b is present in central components of respiratory chemoreflex, such as the nucleus tractus solitarius (NTS). Injection of the neurotoxin substance P‐saporin into NTS destroys Phox2b‐expressing neurons. Impaired hypercapnic ventilatory response caused by this neurotoxin is attributable to a loss of CO2‐sensitive Phox2b‐expressing NTS neurons. A subgroup of Phox2b‐expressing neurons exhibits intrinsic chemosensitivity. A background K+ channel‐like current is partially responsible for such chemosensitivity in Phox2b‐expressing neurons. The present study helps us better understand the mechanism of respiratory deficits in CCHS and potentially locates a brainstem site for development of precise clinical intervention. Abstract The nucleus tractus solitarius (NTS) neurons have been considered to function as central respiratory chemoreceptors. However, the common molecular marker defined for these neurons remains unknown. The present study investigated whether paired‐like homeobox 2b (Phox2b)‐expressing NTS neurons are recruited in hypercapnic ventilatory response (HCVR) and whether these neurons exhibit intrinsic chemosensitivity. HCVR was assessed using whole body plethysmography and neuronal chemosensitivity was examined by patch clamp recordings in brainstem slices or dissociated neurons from Phox2b‐EGFP transgenic mice. Injection of the neurotoxin substance P‐saporin (SSP‐SAP) into NTS destroyed Phox2b‐expressing neurons. Minute ventilation and tidal volume were both reduced by 13% during exposure to 8% CO2 in inspired air when ∼13% of the Phox2b‐expressing neurons were eliminated. However, a loss of ∼18% of these neurons was associated with considerable decreases in minute ventilation by ≥18% and in tidal volume by≥22% when challenged by ≥4% CO2. In both cases, breathing frequency was unaffected. Most CO2‐activated neurons were immunoreactive to Phox2b. In brainstem slices, ∼43% of Phox2b‐expressing neurons from Phox2b‐EGFP mice displayed a sustained or transient increase in firing rate during physiological acidification (pH 7.0 or 8% CO2). Such a response was also present in dissociated neurons in favour of an intrinsic property. In voltage clamp recordings, a background K+ channel‐like current was found in a subgroup of Phox2b‐expressing neurons. Thus, the respiratory deficits caused by injection of SSP‐SAP into the NTS are attributable to proportional lesions of CO2/H+‐sensitive Phox2b‐expressing neurons.