This study aimed to assess the cost-effectiveness of non-vitamin K antagonist oral anticoagulants (NOACs) in comparison with warfarin using data from real practice based on the perspective of the health care system in Thailand. A four-state Markov model encompassing well-controlled atrial fibrillation (AF), stroke and systemic embolism, major bleeding and death was utilised to forecast clinical and economic outcomes. Transitional probabilities, direct medical costs and utilities were derived from the real-world data of the 'COOL-AF Thailand' registry, Thailand's largest nationwide registry spanning 27 hospitals. The cohort comprised AF patients. The primary outcomes assessed were total costs, life years, quality-adjusted life years (QALYs) and the incremental cost-effectiveness ratio. All costs and outcomes were subject to an annual discount rate of 3.0%. A spectrum of sensitivity analyses was conducted. The mean age of the cohort was 68.8±10.7 years. The NOACs group incurred a marginally lower total lifetime cost than the warfarin group (247,857 Thai baht [THB] vs 253,654 THB or 7137 USD vs 7304 USD) and experienced gains of 0.045 life years and 0.043 QALYs over the warfarin group. Given the lower cost and higher benefits associated with NOACs, this implies that NOAC treatment is a dominant strategy compared to warfarin for AF patients. At a ceiling ratio of 160,000 THB (4607 USD) per QALY, NOACs presented a 61.2% probability of being cost effective. Non-vitamin K antagonist oral anticoagulants represent a cost-saving alternative to warfarin in the real clinical practice. However, with a probability of being cost effective below 65%, it suggests some parameter uncertainty regarding their overall cost effectiveness compared to warfarin.