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Background Malaria is a significant public health issue in sub-Saharan Africa, especially in Apac District, Uganda, where it greatly affects children under five. Despite its high rates of morbidity and mortality, there is limited understanding of how communities manage malaria and seek treatment. This study aimed to identify the factors that influence treatment-seeking behaviour among caretakers of young children in Apac District. Methods A cross-sectional analytical study was conducted using quantitative methods, with data collected from 240 households through simple random sampling. Caregivers completed structured questionnaires, and Cox proportional hazards regression analysis was performed in R to examine the socio-economic, demographic, and behavioural factors influencing the time taken by caretakers to seek malaria treatment for their children. Results All caregivers sought treatment for their children and out of the 240 caregivers, (70%) are female. The Cox proportional hazards model identified key factors affecting treatment-seeking time: secondary education significantly increased the likelihood of time for treatment seeking (HR = 1.67, p = 0.044). Significant delays were associated with no medicine at the hospital (HR = 0.61, p = 0.001) and financial constraints (HR = 0.49, p < 0.001). Conclusion To ensure timely malaria treatment for young children, it is crucial to improve drug supply at hospitals and through Village Health Teams, and to educate caregivers on early treatment. Expanding education financing and promoting NGO involvement in caregiver education are essential. Efficient medicine distribution and caregiver education on prompt treatment are key to improving health outcomes for children under five.