OBJECTIVES Systematic anticoagulation management clinic is now recommended to manage warfarinized atrial fibrillation (AF) patient. In Malaysia, the service is recently introduced as pharmacist managed Warfarin Medication Therapy Adherence Clinic (WMTAC). The objective of the present study was to assess the cost effectiveness of anticoagulation clinic in comparison with usual medical in Kuala Lumpur Hospital.  METHODS A Markov model built using the provider perspective and 20 year time horizon was used to assess the cost effectiveness. The base case analysis assumed a cohort of patients with AF 57 years of age with comorbid illnesses. Data sources include a 6 month retrospective cohort analysis of the effectiveness of the clinics, the cost of drugs, cost of personnel and space of the clinics, cost of monitoring and cost of adverse events were obtained from the local source and publications. The transition probabilities of these clinics outcomes were obtained from a literature search. Future costs were discounted by 3% to convert to present values. All costs were in Ringgit Malaysia (RM) based on year 2012.  RESULTS The results of a 20-year period model showed that UMC was dominated by the WMTAC in the same time period. The mean cost of the WMTAC was RM 5864 whereas the UMC cost was RM 6550. The sensitivity analysis showed that clinic treatment costs and effectiveness influenced the cost-effectiveness. If the cost of WMTAC was increased by 50% of the current cost, the WMTAC would not be a dominant intervention. WMTAC was also cost effective for a willingness to pay of RM32000. CONCLUSIONS The anticoagulation management service appears to cost less and provide greater effectiveness than usual care. In conclusion, the Markov model suggests that from the provider perspective the anticoagulation clinic is a more cost effective option than the usual medical clinic in Kuala Lumpur Hospital.