BackgroundFollowing the successful pilot of RTS,S malaria vaccine, it has been recommended by the WHO for prevention of Plasmodium falciparum malaria in children living in endemic areas. Despite the proven benefits of the malaria vaccine, uptake especially of the fourth dose, remains relatively low. We assessed complete uptake of RTS,S malaria vaccine among children 24–59 months and associated factors in the Sunyani Municipality of Ghana. MethodsA cross-sectional study was conducted among 361 caregivers of children aged 24–59 months in the Sunyani Municipality, who had received at least one dose of RTS,S malaria vaccine. Structured questionnaires were administered to caregivers and relevant vaccination information was extracted from the maternal and child health record books. Binary logistic regression analysis was used to determine factors associated with complete uptake of the vaccine at 95 % confidence interval (CI). ResultsApproximately 45 % (164/361) of the children had completed the RTS,S malaria vaccination schedule. Children aged 48–59 months (AOR:0.26, 95 %CI:0.09–0.76), those with caregivers who believed that children were being used for experiment (AOR:0.29, 95 %CI:0.16–0.54) or doubted the safety of the vaccine (AOR:0.27, 95 %CI:0.14–0.52) were less likely to complete the four doses. On the other hand, children of caregivers who reported vaccine shortages and travelled long distances to access immunization services (AOR:3.15, 95 %CI:1.17–8.47), and those with adequate knowledge on the malaria vaccine (AOR:1.89, 95 %CI:1.08–3.29) were more likely to complete the vaccination schedule. ConclusionLess than half of the children who started RTS,S malaria vaccination completed the full schedule. Age of child, caregiver knowledge and perception of the malaria vaccine, and access to immunization service were associated with complete uptake of the RTS,S malaria vaccine. Strengthening caregiver education and access to immunization services could improve uptake of the subsequent doses and coverage of the fourth dose.