Stunting in children less than five years of age is widespread in Sub-Saharan Africa. We aimed to: (i) evaluate how the prevalence of stunting has changed by socio-economic status and rural/urban residence, and (ii) assess inequalities in children’s diet quality and access to maternal and child health care. We used data from nationally representative demographic and health- and multiple indicator cluster-surveys (DHS and MICS) to disaggregate the stunting prevalence by wealth quintile and rural/urban residence. The composite coverage index (CCI) reflecting weighed coverage of eight preventive and curative Reproductive, Maternal, Neonatal, and Child Health (RMNCH) interventions was used as a proxy for access to health care, and Minimum Dietary Diversity Score (MDDS) was used as a proxy for child diet quality. Stunting significantly decreased over the past decade, and reductions were faster for the most disadvantaged groups (rural and poorest wealth quintile), but in only 50% of the countries studied. Progress in reducing stunting has not been accompanied by improved equity as inequalities in MDDS (p < 0.01) and CCI (p < 0.001) persist by wealth quintile and rural-urban residence. Aligning food- and health-systems’ interventions is needed to accelerate stunting reduction more equitably.