AbstractBackgroundSelf‐injurious thoughts and behaviours (SITBs) have been associated with dysfunction of the Autonomic Nervous System (ANS) in children and young people, suggesting that objective ANS measures may aid assessment of suicide risk, but a systematic synthesis of this literature is currently lacking.MethodsFollowing a pre‐registered protocol (PROSPERO CRD42022327605), we conducted a systematic search of PubMed, Medline, Embase, PsycINFO, and Web of Science, for empirical studies published until 10th May 2022 that compared indices of ANS functioning in individuals aged 0–25 years with versus without SITBs, or reported continuous associations between ANS measures and SITBs. Study quality was assessed with the Newcastle‐Ottawa Scales. Pooled effect sizes (Hedge's g) were estimated with random‐effects meta‐analytic models.ResultsTwenty studies (1979 participants) were included in our systematic review, with 16 included in meta‐analyses. Results suggested that SITBs were associated with altered cardiac indices of arousal (g = −0.328, p < 0.001), which was driven by lower heart rate variability in individuals with SITBs (g = −0.375, p = 0.025). Overall results for electrodermal activity were not significant (g = 0.026, p = 0.857), but subgroup analyses showed increased activity in studies of individuals who engaged specifically in non‐suicidal self‐harm (g = 0.249, p = 0.014) but decreased activity in the remaining studies (g = −0.567, p = 0.004).ConclusionsOur systematic review and meta‐analysis found evidence of reduced parasympathetic regulation as well as more tentative evidence of altered electrodermal activity in children and young people displaying SITBs. Future longitudinal studies should test the clinical utility of these markers for detecting and monitoring suicide risk.