Dysregulation of the autonomic nervous system (ANS) may play an important role in the development and maintenance of persistent post-concussive symptoms (PPCS). Post-injury breathing dysfunction, which is influenced by the ANS, has not been well-studied in youth. This study evaluated cardiorespiratory functioning at baseline in youth patients with PPCS and examined the relationship of cardiorespiratory variables with neurobehavioral outcomes. Participants were between the ages of 13-25 in two groups: (1) Patients with PPCS (concussion within the past 2-16 months; n = 13) and (2) non-injured controls (n = 12). Capnometry was used to obtain end-tidal CO2 (EtCO2), oxygen saturation (SaO2), respiration rate (RR), and pulse rate (PR) at seated rest. PPCS participants exhibited a reduced mean value of EtCO2 in exhaled breath (M = 36.3 mmHg, SD = 2.86 mmHg) and an altered inter-correlation between EtCO2 and RR compared to controls. Neurobehavioral outcomes including depression, severity of self-reported concussion symptoms, cognitive catastrophizing, and psychomotor processing speed were correlated with cardiorespiratory variables when the groups were combined. Overall, results from this study suggest that breathing dynamics may be altered in youth with PPCS and that cardiorespiratory outcomes could be related to a dimension of neurobehavioral outcomes associated with poorer recovery from concussion.