Ondo State is one of the States in Nigeria that have taken significant action to reduce the burden of malaria. Specifically, the State currently runs a free health care programme for infants and pregnant mothers as the disease account for most of the maternal and infant deaths record in the country. Given the prevalence of malaria in the morbidity and mortality incidence of Nigeria and the public health care problem it poses, this study attempts to estimate the cost disparity in malaria treatment in private and public hospitals in Ondo State. Using the morbidity statistics of 85249 malaria patients' visit to public hospitals in Ondo State between 2008 and 2013, and responses of 245 patients who had been treated of malaria in public and private hospitals, the finding showed the average cost of treatment to be higher in the private than the public hospitals. The minimum cost for treating malaria in the private and public hospitals were estimated as N1727 and N1203 for the non complicated case and N8900 and N4850 for the complicated cases respectively in the two hospital types. The disparity between the cost groups was observed to be more pronounced in complicated malaria cases. The wide disparity between costs of treatment in the two hospital types worsens the disease burden in the economy. The study suggests narrowing the gap between the treatment costs in the private and public hospitals to increase access to health care.