Caesarean delivery (CD) may reduce placental transfusion and cause poor iron-related haematological indices in the neonate. We aimed to explore the association between CD and anaemia in children aged <5 years utilising data from Demographic and Health Surveys conducted between 2005 and 2015 in 45 low- and middle-income countries (N = 132,877). We defined anaemia categories based on haemoglobin levels, analysed each country's data separately using propensity-score weighting, pooled the country-specific odds ratios (ORs) using random effects meta-analysis, and performed meta-regression to determine whether the association between CD and anaemia varies by national CD rate, anaemia prevalence, and gross national income. Individual-level CD was not associated with any anaemia (OR 0.95, 95% confidence interval (CI) [0.86, 1.06]; I2 = 40.2%), mild anaemia (OR 0.91, 95% CI [0.81, 1.02]; I2 = 24.8%), and moderate/severe anaemia (OR 0.97, 95% CI [0.85, 1.11]; I2 = 47.7%). CD tended to be positively associated with moderate/severe anaemia in upper middle-income countries and negatively associated with mild anaemia in lower middle-income countries; however, meta-regression did not detect any variation in the association between anaemia and CD by the level of income, CD rate, and anaemia prevalence. In conclusion, there was no evidence for an association between CD and anaemia in children younger than 5 years in low- and middle-income countries. Our conclusions were consistent when we looked at only countries with CD rate >15% with data stratified by individual-level wealth status and type of health facility of birth.