Intermittent vagus nerve stimulation (VNS) can reduce the frequency of seizures in patients with refractory epilepsy, but can affect respiration in sleep. Untreated obstructive sleep apnea (OSA) can worsen seizure frequency. Unfortunately, OSA and VNS-induced sleep disordered breathing (SDB) may occur in the same patient, leading to a therapeutic dilemma. We report a pediatric patient in whom OSA improved after tonsillectomy, but coexistent VNS-induced SDB persisted. With decrease in VNS output current, patient's SDB improved, but seizure activity exacerbated, which required a return to the original settings. Continuous positive airway pressure titration was attempted, which showed only a partial improvement in apnea–hypopnea index. This case illustrates the need for clinicians to balance seizure control and SDB in patients with VNS.