National Health Insurance (JKN) is a national coverage health insurance provided by the government in Indonesia. One of the service that is included in JKN is oral health service. According to some news in mass media and previous research, several problems are encountered during this JKN era. The aim of this study was to overview the obstacles that faced by dentists as providers in giving oral health care in Yogyakarta’s primary health center in JKN era. Method:This research was an observasional descriptive study with cross-sectional design. There were 24 dentists as subjects for this research who works in primary health center Yogyakarta city. This research was conducted on August until September 2015 in several primary health centers in Yogyakarta city. Two questionnaires were used as instruments in this research. The first questionnaires was about perception of the dentist’s obstacle and the second was about dentist’s knowledge of JKN system. The datas were analyzed by descriptive statistic method with frequency and mean distribution. Result: Most of the subjects in this research were women (88%), aged 36-45 years old (38%), and worked at the primary health center with non-hospitalized service (79%). Dentist’s obstacles as a providers in JKN in the Yogyakarta’s primary health center were capitation fund (87,5%), oral health’s utility (29%), the benefit package (54%) and dentist’s workloads (46%). The level of dentist’s knowledge about JKN system was mostly good (88%) and moderate (12%). Conclusion: Obstacles faced the dentist that has the highest value in the JKN era in the Yogyakarta’s primary health center is capitation fund. The dentist’s knowledge about the JKN system in the primary health center at Yogyakarta’s city is good.