Objectives: In Burkina Faso, one in every four children under 5 years is stunted. Climate change will exacerbate childhood stunting. Strengthening the health system, particularly the quality of nutrition care at primary health facilities, can minimise the adverse climate effect on stunting. Thus, we examined the quality of nutritional status assessment (QoNA) during curative childcare services in primary health facilities in rural Burkina Faso and its relationship with rainfall-induced childhood stunting. Study design: We conducted a cross-sectional analysis using anthropometric, rainfall, and clinical observation data. Methods: Our dependent variable was the height-for-age z-score (HAZ) of children under 2 years. Our focal climatic measure was mean rainfall deviation (MRD), calculated as the mean of the difference between 30-year monthly household-level rainfall means and the corresponding months for each child from conception to data collection. QoNA was based on the weight, height, general paleness and oedema assessment. We used a mixed-effect multilevel model and analysed heterogeneity by sex and socioeconomic status. Results: Among 5027 young (3e23 months) children (mean age 12 ± 6 months), 21% were stunted (HAZ � 2). The mean MRD was 11 ± 4 mm, and the mean QoNA was 2.86 ± 0.99. The proportion of children in low, medium, and high QoNA areas was 10%, 54%, and 36%, respectively. HAZ showed a negative correlation with MRD. Higher QoNA lowered the negative effect of MRD on HAZ (b ¼ 0.017, P ¼ 0.003, confidence interval ¼ [0.006, 0.029]). Males and children from poor households benefited less from the moderating effect of QoNA. Conclusion: Improving the quality of nutrition assessments can supplement existing efforts to reduce the adverse effects of climate change on children's nutritional well-being.