Costs associated with multidrug-resistant tuberculosis (MDR-TB) are higher than those associated with drug-susceptible TB because of the higher prices of second-line anti-TB drugs, the prolonged duration of treatment, greater productivity loss and higher mortality. The aim of this study was to estimate the cost of treatment for MDR-TB according to the treatment strategy and prognosis in South Korea. We estimated the direct (medical and non-medical) and indirect cost for the treatment of MDR-TB according to the treatment strategies and prognosis: in medically treated, surgically treated and deceased patients groups. The same analyses were undertaken for drug-susceptible TB for comparison. The patients with MDR-TB or drug-susceptible TB were randomly selected from the TB cohort of Seoul National University Hospital, Seoul, South Korea. Direct costs per person were US$4000 (US$2527-4841) in the medically treated group, US$17,457 (US$10,133-26,418) in the surgically treated group and US$33,362 (US$25 386-40 338) in the deceased group. Total costs per person were US$15,856 (US$10,752-38,421), US$47,159 (US$20,587-77,622) and US$478,357 (US$257,377-777,778), respectively. For the patients with drug-susceptible TB, the total cost ranged from US$1680 to US$7637 (median US$2166). The cost for the treatment of MDR-TB is seven to 22 times that of managing the drug-susceptible TB in South Korea. Considering the high cost, transmissibility and considerable fatality of MDR-TB, there is a need to provide specific separate funding for multidrug-resistant tuberculosis.