Health services for pregnancy and delivery at public health facilities are fully subsidized by the government in Mongolia. However, it has been reported that health financing, budget planning, and implementation processes are weak. Therefore, this study aims to estimate the costs per inpatient of vaginal delivery and cesarean section (C-section) by using data gathered from a tertiary hospital in Ulaanbaatar. Inpatient and financial data were collected from the Statistics and Finance, Economics Department of National Center for Maternal and Child Health. A top-down method was used for the calculation of unit costs. The total number of deliveries in 2016 were 11,033, including 7,777 vaginal deliveries and 3,256 C-sections. The cost per inpatient stay for vaginal delivery and C-section were USD 255 and USD 592, respectively. The average cost per bed-day of the six departments of the obstetrics and gynecology hospital was USD 80. The percentage that represents employees' salary in the cost per inpatient was as low as 12.4% for vaginal delivery and 18.5% for C-section, although the cost for salaries accounted for 51.2% of the total expenditure of the hospital. Results show that the cost per inpatient of C-section was two times higher than that of vaginal delivery. The cost of childbirths may account for approximately 9% of total health expenditure of the country. These results may be advantageous to the government in instituting a policy and controlling the health care budget to improve cost-effectiveness and equal access to all in health care services in Mongolia.