The potential benefits and mechanistic effects of working memory training (WMT) in children are the subject of much research and debate. We show that after five weeks of school-based, adaptive WMT 6–9 year-old primary school children had greater activity in prefrontal and striatal brain regions, higher task accuracy, and reduced intra-individual variability in response times compared to controls. Using a sequential sampling decision model, we demonstrate that this reduction in intra-individual variability can be explained by changes to the evidence accumulation rates and thresholds. Critically, intra-individual variability is useful in quantifying the immediate impact of cognitive training interventions, being a better predictor of academic skills and well-being 6–12 months after the end of training than task accuracy. Taken together, our results suggest that attention control is the initial mechanism that leads to the long-run benefits from adaptive WMT. Selective and sustained attention abilities may serve as a scaffold for subsequent changes in higher cognitive processes, academic skills, and general well-being. Furthermore, these results highlight that the selection of outcome measures and the timing of the assessments play a crucial role in detecting training efficacy. Thus, evaluating intra-individual variability, during or directly after training could allow for the early tailoring of training interventions in terms of duration or content to maximise their impact.