Background <p>Cognitively stimulating environments are known to promote the intellectual, socio-emotional and language development of children. Little is known about the relation between cognition and brain structure in young children in low- and middle-income countries (LMICs), particularly in sub-Saharan Africa (SSA) where children are at risk of developmental delay. The overall objective of this study is to measure the association between child stimulation and brain function using neuroimaging techniques and neuropsychological measures.</p> Methods <p>The study will employ an observational follow-up design using a mixed-methods approach. Caregiver-child interaction profiles, children’s developmental scores (<i>N</i> = 980 children) and low-field magnetic resonance imaging (MRI) data (<i>n</i> = 343 children) will be analyzed to understand the relationship between stimulation, developmental outcomes, and brain structure. Associations among the various outcomes will be examined using univariable and multivariable linear regression adjusting for potential confounding factors.</p> Conclusion <p>The findings are expected to provide evidence on the association of the quality, extent and frequency of caregiver-child interactions (child stimulation) and child development with brain structure. The evidence generated will inform policy and practice in the childcare sector. Support, investments or revision of policies and practices will be needed to strengthen the quality of childcare in center-based care.</p> Trial registration <p>The study was registered under PACTR202408640904874 on 27th August 2024.</p>