Background: Deep vein thrombosis and pulmonary embolism are known by the collective name venous thromboembolism. Deep vein thrombosis is the third most common cardiovascular disorder in the world. The disease is also prevalent in Africa including Ethiopia, besides lack of studies that show epidemiology of the disease. Objective: To assess cost effectiveness of rivaroxaban compared to warfarin-based therapy for deep vein thrombosis patients in Ethiopia. Methods: A Markov model was built to compare cost and effectiveness of rivaroxaban 15mg bid for three weeks and 20mg per day for the rest to adjusted dose of warfarin for one year using a restricted societal perspective. The population in this analysis was a hypothetical cohort of deep vein thrombosis patients 40 years old with no contraindication, comorbidity and concomitant therapy. The patients were followed yearly for 24 years up to their average life expectancy. Results: Rivaroxaban therapy resulted in higher quality adjusted life years with a value of 16.78, while warfarin-based treatment resulted in 16.34 quality adjusted life years. Total lifetime costs were $988.58 for rivaroxaban and $932.92 for unfractionated heparin/warfarin. Therefore, rivaroxaban resulted in a gain of 0.443 quality adjusted life years at an additional cost of $55.661. The incremental cost effectiveness ratios for rivaroxaban compared with warfarin was $125.683 per quality adjusted life year saved which is less than willingness to pay threshold of $783 per quality adjusted life year saved. Warfarin resulted in a net monetary benefit of $11,859.72, while that of rivaroxaban is $12,150.82, meaning rivaroxaban is cost-effective. Sensitivity analyses found that the model was sensitive to utility of no deep vein thrombosis, effectiveness of rivaroxaban and cost of rivaroxaban respectively. Conclusion: This study showed that rivaroxaban is a cost effective alternative and substituting rivaroxaban for warfarin is acceptable to willingness to pay threshold.