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Abstract Brain functional connectivity (FC) derived from functional magnetic resonance imaging has been serving as a potential ‘fingerprint’ for adults. However, cross-scan variation of FC can be substantial and carries biological information, especially during childhood. Here we performed a large-scale cross-sectional analysis on cross-scan FC stability and its associations with a diverse range of health measures in children. Functional network connectivity (FNC) was extracted via a hybrid independent component analysis framework on 9,071 participants and compared across four scans. We found that FNC can identify a given child from a large group with high accuracy (maximum >94%) and replicated the results across multiple scans. We then performed a linear mixed-effects model to investigate how cross-scan FNC stability was predictive of children’s behaviour. Although we could not find strong relationships between FNC stability and children’s behaviour, we observed significant but small associations between them (maximumr = 0.1070), with higher stability correlated with better cognitive performance, longer sleep duration and less psychotic expression. Via a multivariate analysis method, we captured larger effects between FNC stability and children’s cognitive performance (maximumr = 0.2932), which further proved the relevance of FNC stability to neurocognitive development. Overall, our findings show that a child’s connectivity profile is not only intrinsic but also exhibits reliable variability across scans, regardless of brain growth and development. Cross-scan connectivity stability may serve as a valuable neuroimaging feature to draw inferences on early cognitive and psychiatric behaviours in children.