Background: Malnutrition continues to affect under-five children in Africa to an overwhelming proportion. The situation is further compounded by the burden of sickle cell disease (SCD). However, association of SCD with stunting, wasting, and underweight in a nationally representative sample of under-five children remains unexplored. We aimed to describe prevalence of undernutrition by sickle cell status, to evaluate its association with growth faltering ascertained with anthropometric indices, and to explore mediating role of hemoglobin.Methods: We availed data from the 2018 Nigeria Demographic and Health Survey (DHS) and the sample comprised 11233 children aged 6–59 months who were successfully genotyped for SCD. The DHS employed a two-stage stratified sampling strategy. SickleSCAN rapid diagnostic test was used for SCD genotyping. Z-scores of length/height-for-age (HAZ), weight-for-height (WHZ), and weight-for-age (WAZ) were computed against the 2006 World Health Organization Child Growth Standards. We fitted logistic regression models to evaluate association of SCD with stunting, wasting, and underweight. Mediation analysis was performed to capture the indirect effect of, and proportion of total effect mediated through hemoglobin level in SCD-anthropometric indices association.Results: Prevalences of stunting, wasting, and underweight among children with SCD were 55.4% (54.5–56.4), 9.1% (8.6–9.7), and 38.9% (38.0-39.8), respectively. The odds of stunting were 2.39 times higher (adjusted odds ratio (aOR) 2.39, 95% CI: 1.26–4.54) among sickle children than those with normal hemoglobin. SCD was also significantly associated with underweight (aOR 2.64, 95% CI: 1.25–5.98), but not with wasting (aOR 1.60, 95% CI: 0.85–3.02). Hemoglobin level significantly mediated SCD-HAZ (adjusted indirect effect (aIE) -0.328, 95% CI: -0.387, -0.270), SCD-WHZ (aIE − 0.080, 95% CI: -0.114, -0.050), and WAZ (aIE − 0.245, 95% CI: -0.291, -0.200) associations. The extent of mediation was highest for SCD-HAZ association (adjusted proportion mediated 0.928, 95% CI: 0.535–2.770).Conclusion: We presented compelling evidence of the negative impact of SCD on nutritional status of under-five children. Integration of a nutrition-oriented approach into a definitive SCD care package and its nation-wide implementation could bring promising results by mitigating the nutritional vulnerability of children with SCD.