Malaria is one of the major public health problems in Malawi, contributing to the majority of morbidity and mortality among children under five. Ignorance of malaria symptoms results in delayed treatment, which often degenerates into fatal emergencies. This study analyzed the impact of maternal malaria knowledge on healthcare preferences and timeliness of treating children with reported fever. The Malaria Indicator Survey data for 2012, which were adequately weighted, were analyzed using multinomial logit and Poisson regression models. The results showed low maternal average years of formal education (3.52) and average mothers’ age was 27.97 years. Majority of the women (84.98%) associated fever with malaria, while 44.17% associated it with chilling. Also, 54.42% and 32.43% of the children were treated for fever on the same day and the following day that fever started, respectively. About 9.70% paid for fever treatment from their regular incomes, while 51.38% sought treatment from either public or private health centers. Multinomial Logit regression results showed that relative to using of other treatments, probabilities of selecting private hospitals and public health centers increased with age of the household heads, resident in urban areas, mothers’ years of education, number of days taken off for treatment, paying medical bills from regular, occasional and borrowed incomes, and knowledge of diarrhea and shivering as symptoms of malaria. In the Poisson regression results, timeliness of seeking treatment was significantly enhanced by knowledge of fever as malaria symptom, residence in northern and central regions of Malawi and use of income from sale of assets to pay medical bills (p < 0.10).However, delays in treating children was motivated by age of the household heads, number of days taken off to care for sick child and usage of regular, borrowed and other incomes to pay medical bills. (p < 0.05). It was concluded that efficiency of public sector in treating malaria holds significant prospects for fighting malaria in Malawi. However, adequate efforts should be channeled in enhancing the knowledge of women on malaria symptoms, among others.