BackgroundMalnutrition in childhood has lasting consequences; its effects not only last a lifetime but are also passed down from generation to generation such as short stature, school-aged children are the most vulnerable section of the population and require special attention, including nutrition.MethodWe searched Medline through PubMed, Scopus, and Web of Science to identify all observational studies published before Jun 2022. Observational studies with a pediatric population aged 5–18 years that evaluated risk estimate with 95% confidence intervals the relationship between dietary diversity and undernutrition (wasting, stunting, and thinness) were included. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) were followed.ResultsThis is a first systematic review and meta-analysis with a total of 20 studies were eligible (n = 18 388). Fourteen data evaluated stunting resulting in a pooled effect size estimated odds ratio of 1.43 (95% CI: 1.08–1.89; p = 0.013). Ten data evaluated Thinness resulting in a pooled effect size estimated odds ratio of 1.10 (95% CI: 0.81–1.49; P = 0.542). Two studies were revealed wasting with a odds ratio of 2.18 (95% CI: 1.41–3.36; p-value < 0.001).ConclusionAccording to the conclusions of this meta-analysis of cross-sectional studies, inadequate dietary diversity increases the risk of undernutrition in growth linear but not in thinness in school-aged children. The findings of this analysis suggest that initiatives that support improvements to the diversity of children’s diets to reduce the risk of undernutrition may be warranted in LMICs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04032-y.