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Background and objective: Frequent central apnoeas are sometimes observed in healthy children; however; the pathophysiology of an elevated central apnoea index (CAI) is poorly understood. A raised CAI may indicate underlying ventilatory control instability (i.e. elevated loop gain, LG) or a depressed ventilatory drive. This pilot study aimed to compare LG in otherwise healthy children with an elevated CAI to healthy controls. Methods: Polysomnographic recordings from children (age > 6 months) without obstructive sleep apnoea and with a CAI > 5 events/h (n = 13) were compared with age and gender‐matched controls with a CAI < 5 events/h (n = 13). Spontaneous sighs were identified during non‐rapid eye movement (NREM) sleep, and breath–breath measurements of ventilation were derived from the nasal pressure signal. A standard model of ventilatory control (gain, time constant and delay) was used to calculate LG by transforming ventilatory fluctuations seen in response to a sigh into a ventilatory‐drive signal that best matches observed ventilation. Results: The high CAI group had an elevated LG (median = 0.36 (interquartile range, IQR = 0.35–0.53) vs 0.28 (0.23–0.36); P ≤ 0.01). There was no difference in either the time constant (P = 0.63) or delay (P = 0.29) between groups. Elevated LG observed in the high CAI group remained after accounting for degree of hypoxia (average oxygen saturation (SpO2) during each analysable window) experienced (0.40 (0.30–0.53) vs 0.25 (0.23–0.37); P = 0.04). Conclusion: An elevated CAI in otherwise healthy children is associated with a raised LG compared to matched controls with a low CAI, irrespective of level of hypoxia. This relative ventilatory instability helps explain the high CAI and may ultimately be able to help guide diagnosis and management in patients with high CAI. While central apnoeas are common in children, a central apnoea index of >5 events/h is outside normal ranges and raises concern regarding origins of such events. Our study indicates that an elevated index of >5 is associated with a hypersensitive ventilatory control system and supports literature that neuroimaging may not be needed. [ABSTRACT FROM AUTHOR]