Background: Malaria has remained one of the leading causes of morbidity and mortality in children despite effective preventive and treatment modalities. This study is aimed at looking at the malaria preventive practices among under-five children in three Niger Delta states in Nigeria and comparing the differences among them if any. Methods: This was a cross sectional study carried out over six months from 1st January to 30th June 2019 in public health facilities among under-five children in three South-South states (Akwa Ibom, Delta and Rivers) of Nigeria. Using a stratified sampling method, children were recruited from 36 health facilities in the three states. A pretested interviewer administered questionnaire was used to harvest relevant information on socio-demographic characteristics of the subjects and informants and malaria preventive practices. Obtained data was analysed using SPSS version 22 and results are presented in prose and frequency tables. Chi-square and Fischer’s exact were used for comparison of categorical variables, while a p-value of ± 1.06 years. Mothers constituted over 80% of the informants in all the states. More of the informants had secondary education in Akwa Ibom and Delta states, while in Rivers state, more of them had tertiary education. Malaria prevention method practiced in the three states included; use of insecticide treated bed net (ITNs), insecticide spray, anti-malarial drugs, clearing of bushes and disposal of mosquito breeding cans and use of mosquito repellents. Indoor residual spraying (IRS) was not practiced in any of the states. Use of ITN was practiced more in Rivers state (53.2%) than in Delta (20.3%) and Akwa Ibom (8.2%) states, while use of insecticide spray was commoner in Akwa Ibom state (77.2%) than in Delta (56.3%) and Rivers (42.4%). This difference in the prevention techniques practiced among the states was statistically significant (Fischers exact −724.2, p-value = 0.0001). Conclusion: In conclusion, the practice of ITNs use is low in South-South Nigeria with IRS not being practiced at all. Introduction of IRS as a method of malaria vector control and public health education on ITNs ownership and use is advocated.