Globally, malaria continues to have clinical importance and economic impact. There is insufficient data on direct medical costs of malaria treatment at healthcare facilities since the adoption of artemisinin combination therapies (ACTs) in Nigeria. The study aimed to assess the direct medical cost incurred by patients with uncomplicated malaria disease after the adoption of ACTs. The study was retrospective. Data were collected from malaria patients' folders between January 2014 and June 2018 in two secondary hospitals. Costing was carried out using the National Health Insurance Scheme price list (second edition). Descriptive statistics, measures of central tendency, and dispersion were used. A total of 2,420 patient folders were assessed. The prevalence of uncomplicated malaria increased every year, with 2017 having the highest number (n = 754). The average direct medical cost incurred per patient for the treatment of uncomplicated malaria treatment was 2,234.07 ± 1,307 NGN (US $5.8) which accounts for 12.4% of the national minimum wage earnings. About a third (64.6%) of the patients were treated with artemether-lumefantrine tablets. The mean cost of antimalarial drugs per treatment episode was 748.87 ± 336.75 NGN (US $1.96). The direct cost of malaria treatment was high contributing to the significant economic burden even after the adoption of ACTs in Nigeria.