This study was conducted to analyze if there is a difference between the head hospital and branch hospital by comparing the profitability and operating expenses to patient revenue of oriental medicine hospitals affiliated with universities in order to find whether opening branch hospitals is an appropriate method to increase profitability. Profit indices used for the comparison of head hospital and branch hospital include ratio of operating profit on medical revenue, net-income on medical revenue, net profit to total assets, and operating profit to total assets; and cost indices included ratio of labor costs, material costs and administrative costs. In comparison of profit indices of head hospitals and branch hospitals, head hospitals displayed negative(-) in all four profit index averages while branch hospitals displayed positive(+), showing that branch hospitals have higher profitability. In particular, in the case of head hospitals, ratio of net profit to total assets was -13.6%, while that of branch hospitals was 12.9%, which was higher than 3.1%, the average of Korean oriental medicine hospitals in 2011. As a result of difference analysis between groups of head hospitals and branch hospitals, profit indices of ratio of operating profit on medical revenue, net-income on medical revenue, and ratio of net profit to total assets were found to vary by hospitals, but there was no statistically significant difference between head hospitals and branch hospitals(p<0.1). Only the ratio of operating profit to total assets of head hospitals and branch hospitals indicated significant difference between the two groups, showing that ratio of operating profit to total assets of branch hospitals is larger than that of head hospitals. Meanwhile, the cost indices of ratio of labor costs, material costs and administrative costs in the difference test results did not show significant difference between the head hospital and branch hospital(p<0.1). Thus, it cannot be said that a certain oriental medicine hospital's profitability is high or low depending on whether it is head hospital or a branch as profitability varies depending on the management environment of the hospital. Therefore, oriental medicine hospitals affiliated with universities would need to make efforts to increase their profitability as an individual hospital rather than focusing on whether they are head hospital or a branch.