Malaria remains a significant global health burden affecting millions of people, with children under 5 years and pregnant women most vulnerable. Recently, World Health Organization (WHO) introduced, the RTS,S/AS01 malaria vaccine as an intervention strategy with implementation in three countries of Malawi, Kenya and Ghana. The factors influencing the uptake of malaria vaccine is relatively unknown in implementing areas. In Malawi, Nsanje District reported low coverage (60%) of fully immunized children with malaria vaccine in 2021, way below the recommended WHO target coverage of 80%. This study therefore explored the factors influencing the uptake of malaria vaccine among children aged 24-36 months in Nsanje District. The study investigated; how mother/caregiver factors, health care system factors, child factors and community factors influence the uptake of the malaria vaccine. A cross section study design was used and interviews conducted on 410 participants using a questionnaire. Data analyses included descriptive statistics and logistic regression to determine the factors that influence malaria vaccine uptake. Uptake of malaria vaccine was 90.5% for dose one, but reduced to 87.6%, 69.5% and 41.2% for dose two, three, and the booster, respectively. Timeliness of RTS,S one was 69.7%, 64.6% for RTSS two, 56.7% for RTS,S three and 48.3% for RTS,S four. Highest delay timeliness on uptake was noted on RTS,S dose four (51.7%). The dropout rate for malaria vaccine was 23.2%. Children of caregivers with secondary or upper education and who attended ANC four times or more had increased odds of full uptake of malaria vaccine [OR:2.43, 95%CI:1.08-6.51, p-value=0.033, and OR: 1.89, 95%CI 1.18 - 3.02, p-value=0.008, respectively]. Children who ever suffered adverse effects following immunization and those who traveled long distances to reach the vaccination centre had reduced odds of full uptake of malaria vaccine [OR: 0.35, 95%CI: 0.06-0.25, p- value<0.001 and OR:0.30, 95%CI:0.03-0.39, p-value <0.001, respectively]. Only 18% (n=65) knew the correct schedule for vaccination and 45.8% (n=158) knew the correct number of doses a child was to receive. Only RTS,S dose one uptake met the WHO targets and the mothers/caregivers have low level of information regarding malaria vaccine, especially on the dosing schedule. Further, the mothers/caregivers had low level of information regarding malaria vaccine, especially on the dosages and the scheduled months. Recommendation is that Nsanje District Health Directorate should strengthen communities education about malaria vaccine to increase its uptake.