Background Malaria is one of the significant health problems in the world, and the greatest burden of the disease is concentrated in Africa, which accounts for about 95% of cases. The World Health Organization indicates that early seeking for treatment is crucial to avoid worsening the disease and, consequently, death. This work evaluated the factors that influence early health care-seeking (EHCS) behaviour in children under five years old and the effect of EHCS on hospitalisations.

Methods We conducted a health facility-based observational longitudinal study over 5 years, starting in January 2015 where confirmed P. falciparum (Pf) malaria cases were identified in an ongoing morbidity surveillance system established in Manhiça district hospital and 5 referral health centres by Manhiça Health Research Centre. Using the first visit for all children that visited a Health Facility (HF) with fever or history of fever in the previous 24 hours and confirmed Pf malaria, we defined EHCS as a visit to an HF within 48h after the onset of fever. We used multilevel logistic regression to identify the factors related to EHCS and the association between EHCS and hospitalisation.

Results Of 66620 under 15 years old children screened only 1603 meet all inclusion criteria. A kilometre increase in the distance to a health facility reduced the odds of EHCS by 11% (aOR=0.89; CI: [0.83–0.95]; p=0.001). EHCS reduced the odds of hospitalization (aOR=0.56; 95% CI: [0.34 -0.93]; 0.024) and year increase in the year of the visit increased the odds of hospitalization by 66% (aOR = 1.66; 95% CI: [1.41–1.93]; p<0.001).

Conclusion Increasing the distance to HF reduced the likelihood of EHCS, whereas EHCS reduced the risk of hospitalisation. Maulana and Calanga lead the hospitalisation cases in the study area in children with malaria and cases of delay in health care seeking.