Indonesian Case Based Groups (INA-CBGs) implementation on hospital financing for stroke patient using Jaminan Kesehatan Masyarakat (Jamkesmas) at 3rd class hospitalization requires therapy plan management and cost analysis. The study objectives was to determine the suitability cost between real stroke treatment cost and health financing based on INA-CBGs. This cross sectional observational study used retrospective sampling method. The subjects were taken from all stroke patient population using Jamkesmas insurance at Jogja Hospital, were hospitalized between January 2011-April 2012. Patient’s length of stay and costs were defined as study variable. Data was analysed using descriptive analysis and Mann Whitney test. Throuh this study we conclude the average rate of real stroke treatment cost at Jogja Hospital was higher insignificantly than INA-CBGs based cost.