OBJECTIVES: The INA-CBG’s (Indonesia Case Based Groups) package rate implementation for National Health Insurance Programme member since 1st January 2014 suffering from stroke has enforced the all hospital in Indonesia to do a quality control and efficient service cost. A cost analysis study was needed to prevent hospital loss. This study aimed to find out the discrepancy of the real stroke treatment cost averagely in first, second, and third class of stroke patient hospitalization in PKU Muhammadiyah Yogyakarta with INA-CBG’s rate based on the 69th Minister of Health’s Rule in 2013. METHODS: This study was an observational study with cross sectional design. Data collection was done retrospectively. The study subjects were all hospitalized stroke patients whose members of National Health Insurance registered between January to June 2014. Study data were in real direct medical and non-medical cost analysed for its suitability with INA-CBG’s rate. Data analysis was done using descriptive statistic test and t-test. RESULTS: Data results showed no significant discrepancies were found between average real cost of first class hospitalization and INA-CBG’s rate with code of G-4-14-I (sig. 0,566), G-4-15-I (sig. 0,121), G-4-15-II (sig. 0,090), and G-4-15-III (sig. 0,625). No significant discrepancies were found between average real cost of second class hospitalization and INA-CBG’s rate with code of G-4-14-II (sig. 0,180) and G-4-15-II (sig. 0,655). The discrepancies were statistically significant between average real cost of third class hospitalization and INA-CBG’s rate with code of G-4-14-II (sig. 0,000) and G-4-15-II (sig. 0,026), and no significant discrepancies with code of with the code of G-4-14-I (sig. 0,180) and G-4-15-I (sig. 0,500). CONCLUSIONS: The conclusion of this study was no significant discrepancies were found between average real cost of stroke treatment hospitalization and INA-CBG’s rate. Thus, the hospital was adequately capable of managing stroke treatment cost based on INA-CBGs.