Background Weather and climate-related disasters, including floods, impact undernutrition through multiple pathways, including food security, inadequate child care practices, and water and sanitation. This review aimed to provide systematic evidence of the impact of floods on undernutrition in children under five years of age in Low and Middle-income countries (LMICs). Methods We searched PubMed, Web of Science, Embase, MEDLINE, CINAHL and Scopus for peer-reviewed articles. Popline, WHO Library database (WHOLIS), the International Disaster database (EM-DAT), Food and Agriculture Organisation (FAO), UNICEF and Eldis were searched for grey literature articles. Database searches were first conducted in 2016 and updated in 2020. We included English language articles that reported the effect of floods on undernutrition outcomes in children under 5 years of age in LMICs, without limitation to study design and year of publication. The quality of selected studies was assessed using the National Institutes of Health (NIH) tool for Observational Cohort and Cross-Sectional Studies. Results Of the 5701 articles identified, 14 met our inclusion criteria. The review noted stunting as the most frequently reported significant form of undernutrition in flood-affected areas. Severe and recurrent floods showed the greatest impact on undernutrition. Due to weak and limited evidence, the study is inconclusive on the most significant forms within the short-term and intermediate periods following floods. On the other hand, stunting was noted as the most frequently reported significant form of undernutrition in the long-term period following floods. There was generally little evidence of the effect of floods on micronutrient deficiencies. Factors associated with child undernutrition in the flood-affected areas included age, gender, diarrhoea, maternal and paternal education, maternal age, household size, land ownership and socioeconomic status. Overall, the quality of the evidence was fairly weak, with the main challenge lying in the inability of the studies to establish causal pathways for the observed effects. Conclusions The review suggests clear plans and strategies for preventing and reducing the long-term impact of floods on undernutrition in children under five years. Future research utilising long-term prospective data is indispensable to provide more robust evidence to guide better prevention measures, response decisions and interventions.