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Background Diarrhoea is one of the leading causes of death among children under 5 years old in the Democratic Republic of the Congo (DRC). Despite positive effects on prognosis, there is limited literature about the healthcare-seeking behaviours of children with diarrhoea, especially in the DRC. This study used the Andersen Behavioural Model, a theoretical framework, which was commonly adopted to study healthcare utilisation, to investigate and predict factors associated with the use of healthcare to treat diarrhoea in the DRC. Methods Data collected from 2626 under-five children with diarrhoea in the last 2 weeks from the Multiple Indicators Cluster Survey conducted by the National Institute of Statistics in 2017–2018, in collaboration with the United Nations Children’s Fund were used in this study. Both direct and indirect relationships among four latent variables: predisposing traits, enabling resources access, health needs, and health services use were measured using the structural equation modelling to test the Andersen behavioural model. The confirmatory Factor Analysis model was also modified based on the DRC context to explore this further. Results The modified model had the goodness of fit index (GFI) of 0.972, comparative fit index (CFI) of 0.953 and RMSEA of 0.043 (95% CI: 0. 040, 0.047). Health needs (especially diarrhoea) had the largest positive direct effect on healthcare utilisation (standardized regression coefficient [β] = 0.135, P P = 0.015). Health needs also emerged as a mediator for the positive effect of predisposing on utilisation (indirect effect, β = 0.014; P = 0.009). Conclusion Access to improved water and improved sanitation, as well as socioeconomic factors like household wealth, were significantly associated with health-seeking behaviours for diarrhoea treatment in the DRC. Besides, caregivers who own higher levels of educational attainments were more inclined to have positive health services uses during the treatments. Efforts are needed to enhance the oral rehydration therapy coupled with educating caregivers on its appropriate use.