In February 2018, the Ministry of Food and Drug Safety in Korea approved tenofovir disoproxil fumarate and emtricitabine (TDF/FTC) co-formulate for use in pre-exposure prophylaxis (PrEP) for the prevention of human immunodeficiency virus (HIV) infection. This study aimed to estimate the cost-effectiveness of PrEP in men who have sex with men (MSM), a major risk group emerging in Korea. A dynamic compartmental model was developed for HIV transmission and progression in MSM aged 15-64 years. With a combined model including economic analysis, we estimated averted HIV infections, changes in HIV prevalence, discounted costs, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios (ICERs). PrEP was evaluated in both the general MSM and high-risk MSM populations and was assumed to reduce infection risk by 80%. Implementing PrEP in all MSM would avert 75.2% HIV infections and facilitate a gain of 37,372 QALYs at a cost of $274,822 per QALY gained over 20 years relative to the status quo. Initiating PrEP in high-risk MSM with an average of eight partners per year (around 20% of MSM) would improve the cost-effectiveness, averting 78.0% HIV infections and add 29,242 QALYs at a cost of $51,597 per QALY gained, which is within the willingness-to-pay threshold for Korea of $56,000/QALY gained. This result was highly sensitive to annual PrEP costs, quality-of-life for people who are on PrEP, and initial HIV prevalence. Initiating PrEP in a larger proportion of MSM in Korea would prevent more HIV infections, but at an increasing cost per QALY gained. Focusing PrEP on higher risk MSM and any reduction in PrEP cost would improve cost-effectiveness.