We present data on factors associated with poor treatment outcome (death or recovery with a neurological complication) among children treated for malaria in Ibadan, Nigeria. A total of 2468 children (1532 with uncomplicated and 936 with severe malaria) were recruited from three government facilities. History was obtained from caregivers and malarial parasite test was carried out on each child. About 76.0% of caregivers had instituted home treatment. Following treatment, 2207 (89.5%) children recovered without complications, 9.1% recovered with neurological complications, and 1.4% died. The possibility of poor treatment outcome increased with decreasing child’s age (). A statistically significant proportion of children with pallor, jaundice, hepatomegaly, splenomegaly, respiratory distress, and severe anaemia had poor treatment outcome. Following logistic regression, child’s age < 12 months compared to older age groups (O.R = 5.99, 95% C.I = 1.15–31.15, and ) and loss of consciousness (O.R = 4.55, 95% CI = 1.72–12.08, and ) was significantly associated with poor treatment outcome. We recommend interventions to improve caregivers’ awareness on the importance of seeking medical care early. This will enhance early diagnosis and treatment and reduce the likelihood of complications that lead to poor treatment outcomes.