BackgroundMalaria remains a major public health burden to children under five, especially in Eastern Africa (E.A), —a region that is also witnessing the increasing occurrence of floods and extreme climate change. The present study, therefore, explored the trends in floods, as well as the association of their occurrence and duration with the malaria incidence in children < 5 years in five E.A partner countries of Forum for China-Africa Cooperation (FOCAC), including Ethiopia, Kenya, Somalia, Sudan, and Tanzania between 1990 and 2019.MethodsA retrospective analysis of data retrieved from two global sources was performed: the Emergency Events Database (EM-DAT) and the Global Burden of Diseases Study (GBD) between 1990 and 2019. Using SPSS 20.0, a correlation was determined based onρ= -1 to + 1, as well as the statistical significance ofP= < 0.05. Time plots of trends in flooding and malaria incidence were generated in 3 different decades using R version 4.0.ResultsBetween 1990 and 2019, the occurrence and duration of floods among the five E.A partner countries of FOCAC increased and showed an upward trend. On the contrary, however, this had an inverse and negative, as well as a weak correlation on the malaria incidence in children under five years. Only Kenya, among the five countries, showed a perfect negative correction of malaria incidence in children under five with flood occurrence (ρ =-0.586**,P-value =0.001) and duration (ρ =-0.657**,P-value = <0.0001).ConclusionsThis study highlights the need for further research to comprehensively explore how different climate extreme events, which oftentimes complement floods, might be influencing the risk of malaria in children under five in five E.A malaria-endemic partner countries of FOCAC. Similarly, it ought to consider investigating the influence of other attributes apart from flood occurrence and duration, which also compound floods like displacement, malnutrition, and water, sanitation and hygiene on the risk and distribution of malaria and other climate-sensitive diseases.