BackgroundAnaemia, malaria, and stunting remain health problems, especially in children younger than five years, and those conditions are linked to morbidity and mortality. The main objective was to assess the relationships between anaemia, malaria, and stunting. Also, the current study aimed to understand the complex interrelationships between explanatory factors, and their direct or indirect relationship with childhood malaria, anaemia, and stunting in Burundi. MethodsThe study used secondary data from the Demographic and Health Survey in Burundi (BDHS) conducted on the March 7, 2017, with a weighted sample size of 13611 children younger than five years. A multivariate structural equation model (SEM) was used to evaluate the interrelationships between dependent variables and their direct or indirect relationship with childhood malaria, anaemia, and stunting. SEMs diverge from other techniques, as they look at the effects on hypothesised relationships from both direct and indirect perspectives (Takele et al., 2023) [1]. The variables with statistical significance were set at a p-value <0.05. ResultsThe findings from this study indicated an association between anaemia, malaria, and stunting (p < 0.001). The environmental and household factors were statistically significant (p < 0.038 and p < 0.001 respectively) and positively impacted childhood malaria, anaemia, and stunting. The results also indicated that the household factors were statistically significant (p < 0.001) predictors of childhood malaria, anaemia, and stunting. Furthermore, the findings from this study revealed that geophysical factors have a positive significant (p < 0.001) impact on childhood malaria, anaemia, and stunting via the mediating of the household factors. Contrastingly, with the environmental factors as a mediator, we observe a negative significant (p < 0.001) impact on childhood malaria, anaemia, and stunting. Lastly, the results showed that demographic factors had a negative significant (p = 0.004) effect on childhood anaemia, malaria, and stunting via the mediating of household factors. ConclusionThe findings from this study revealed an association between malaria, anaemia, and stunting, which imply that these conditions could contribute to collaborative improvements in child well-being. In addition, child demographic, household, environmental, and geographic factors were direct and indirect important drivers of childhood malaria, anaemia, and stunting. Therefore, improving sanitation, access to clean water, nutrition practices, and health care, especially for children from rural areas, and uneducated mothers with poor backgrounds could help to control and eliminate stunting, anemia, and malaria in children younger than five years in Burundi.