Background : Primary health center is one of primary health care that works together with The Indonesidan National healthcare security called BPJS Kesehatan that provides comprehensive health service in Indonesian national health insurance system (JKN). There are obstacles that happen in the run of JKN. One of them is about capitation fund. According to ministry of health regulation No. 69 2013, the capitation fund set to puskesmas is Rp. 3.000-Rp 6.000,-. There are health providers who think that the capitation fund is still not enough. The aim of this study is to overview perception of dentists about capitation fund from different aspects, such as: workload, duration of service time, wage, and minimum service standard in Indonesian national health insurance (JKN) at primary health center in the Yogyakarta city. Methods : Research method was observational descriptive study with the cross-sectional approach. The research subjects were 35 dentists who work at primary health center in Yogyakarta city. Sampling technique used in this research was total sampling technique. Instrument used in this research was questionnaire of perception. The data were analysed using descriptive statistic method. Result : The result showed that based on workload aspect, 84% of dentists disagreed with the capitation fund, based on duration of service time, 69% of dentists agreed with the capitation fund, based on wage, 76% of dentists agreed with the capitation fund, and based on minimum service standard, 66% of dentist agreed with the capitation fund. Conclusion : It can be concluded that based on workload aspect, most of dentists disagreed with capitation fund set to puskesmas Rp. 3.000-Rp. 6.000,-