While the national prevalence of child stunting has been decreasing, Mexico has yet to reduce stunting equitably across rural and indigenous communities. We estimated the prevalence and distribution of child stunting in children aged < 5 years by rural and urban areas as well as described and compared the household factors associated with child stunting in both settings. We used data on 3910 children aged < 5 years from the latest nationally representative health and nutrition Mexican survey (2018–2019). We found evidence that child stunting in Mexico has plateaued, halting the successful decline that had been observed in previous decades and being a pervasive marker for health inequities. We identified higher odds for child stunting among rural areas (adjusted odds ratio (AOR) 1.81, 95% confidence interval (CI) 1.12–2.91), and in rural indigenous households (AOR 2.08, 95% CI 1.38–3.13). Household education was the only consistent protective factor against stunting across rural/urban settings (AOR 0.35, 95% CI 0.17–0.72; AOR 0.45, 95% CI 0.21–0.96, correspondingly). Policy-makers, researchers, and stakeholders need to aim efforts toward implementing evidence-based, culturally sensitive, and sustainable policies and interventions at rural areas mostly in the southern region and among rural indigenous households, including a strong component to achieve higher household education.