Background: Development of health system in Indonesia based on the national health system (SKN). The national health subsystem is a subsystem of financing. To protect the people from financial risks are needed healths financing prepaid systems. There are some patients assumed that the quality of service of direct payment system and payment by health insurance are distinguished. The purpose to determine the differences between the quality of service payment system INA-CBGs With Fee For Service inpatients class II at PKU Muhammadiyah Hospital Bantul. Method: This study used descriptive method. The population research was inpatients class II at PKU Muhammadiyah Hospital Bantul. The sample size on the payment systems INA-CBG 50 respondents and Fee For Service 50 respondents. The method of data collection using questionnaires. Data analysis performed by different test averrage to the independent samples using Mann-Whitney method. Result and Discussion: Patients assume the quality of service at PKU Muhammadiyah Hospital in Bantul distinguished between fee for service financing and INA-CBGs. They think fee for service financing get better service than financing by health insurance. Statistics showed the mean rank of INA-CBGs is 44.41 and the mean rank of Fee For Service is 56.59. Different test average result to the independent samples using Mann-Whitney method indicate there is significant differences between the payment system INA-CBGs with Fee For Service to quality of service. This differences is due to the large number of INA-CBGs patients. This is because the communication aspect, long queues and administration become complicated so that patients are not satisfied. Conclusions: There are significant differences between the quality of service payment system INA-CBGs With Fee For Service