Background: Non-vitamin K antagonist oral anticoagulants (NOACs) are effective alternatives to warfarin for stroke prevention in non-valvular atrial fibrillation (NVAF) patients. However, concerns have arisen due to their higher costs than warfarin. Aim: To estimate and compare the total direct medical costs of warfarin, dabigatran and rivaroxaban treatments in NVAF patients in Penang general hospital. Methods: This was a retrospective study capturing one year of data from January to December 2015. The data were extracted from hospital records. The total direct medical costs, including any costs associated with treatment-related complications, were calculated as the sum of drug acquisition cost, INR point-of-care testing cost, personnel cost and treatment-related complications cost. Descriptive statistical analysis was performed to describe the results. Results: A total of 224 patients (warfarin, n = 122; dabigatran, n = 63; rivaroxaban, n = 39) were recruited. The total direct medical costs including cost of any treatment-related complications for warfarin ranged from MYR1269.77 to MYR2383.35. The total direct medical costs with treatment-related complications for dabigatran and rivaroxaban were MYR3469.18 and MYR2883.35, respectively. During the study period, one ischaemic stroke (0.82%) and three major bleeding events (2.46%) were observed in the warfarin group, whereas only one patient (1.59%) in the dabigatran group experienced minor bleeding. Drug acquisition costs for NOACs were high, which accounted for 80% of the total direct medical costs in the dabigatran group. However, the direct medical costs for warfarin increased by 4-fold when treatment-related complications costs were included. Conclusion: The direct medical costs of NOACs were relatively higher than warfarin, however, the incidence of major bleeding was higher in the warfarin group.