We aimed to evaluate the cost-effectiveness of the cytochrome p450 (CYP) 2C19 genotype-guided antiplatelet therapy compared with using clopidogrel or prasugrel without considering genotypes in patients with acute coronary syndrome undergoing percutaneous coronary intervention in Korea. We performed a cost-effectiveness analysis using a decision analytic model with a one-year time period employing a societal perspective. A cohort of 10,000 patients was assigned to each treatment alternative as follows: (1) selecting antiplatelet therapy between clopidogrel and prasugrel utilizing the genotype information of CYP2C19; (2) using clopidogrel without using genotype information; (3) using prasugrel without using genotype information. The primary outcome measure was the incremental cost per effectiveness ratio (ICER), where the effectiveness was defined as a death or cardiovascular event avoided, comparing genotype-guided therapy with the other two alternatives. The cardiovascular event was defined as any occurrence of nonfatal myocardial infarction, nonfatal stroke, and bleeding. The secondary outcome measures were the incidence of each event for each alternative and the number needed to treat (NNT) with the genotype-guided therapy versus each of other alternatives. The treatment strategy of genotype-guided therapy was dominant when compared with using clopidogrel (ICER: −36,610,303 KRW, −33,282 USD) or prasugrel (ICER: −24,202,531 KRW, −22,002 USD) for all patients without considering the genotype. The NNT of the genotype-guided therapy versus clopidogrel and prasugrel for all patients was 26 and 12, respectively, for any occurrence of death and cardiovascular event. Genotype-guided antiplatelet therapy in patients with acute coronary syndrome appeared to be a cost-effective treatment strategy in Korean patients.