Childhood exposure to interparental intimate partner violence (i-IPV) is a pervasive form of child maltreatment, posing major public health concerns and elevating risks for enduring adverse clinical and developmental consequences. However, assessing the full spectrum of clinical effects is challenging, potentially leading to inconsistent identification of children in need of early intervention. This systematic review aimed to identify hypothalamic-pituitary-adrenocortical axis dysfunction following i-IPV exposure, elucidating the underlying biopsychobehavioural mechanisms and predicting adverse outcomes. We searched Embase, MEDLINE, and PsycINFO for peer-reviewed studies from infancy through adolescence, screened reference lists and conducted forward searches. Analysis of 23 publications (N = 1848) revealed associations between i-IPV and altered adrenocortical function from early childhood, influenced by FKBP5 haplotype, parental caregiving and offspring emotional insecurity. Results showed that the adrenocortical stress response may predict internalising and externalising problems, childhood asthma, impaired executive function and poor academic performance. Nonetheless, inconsistencies in findings between studies suggest methodological heterogeneity and potential bias. Identifying biomarkers such as cortisol can enhance prediction and mechanism-based intervention efforts but long-term studies with a common theoretical and methodological framework are needed for comprehensive understanding. Integrating biological, emotional, and behavioural assessments could potentiate trauma services and research, ultimately improving outcomes for affected children.