Stroke is a major health problem causing 75.2% of mortality and 81.0% of disability in developing countries. It accounts for the primary causes of Indonesian deaths (15.4%). This research aims to analyze the variation of medicines costs for inpatient ischemic stroke based on the hospital, patients, and prescribing characteristics. Retrospective data were collected from January-September 2019 by reviewing medical records of living patients on discharge. The number of complete data for analysis is 443 entries from 23 hospitals in 5 regionals of Indonesia which are transferred to the SPSS program for further analysis. The result shows that all hospital characteristics, either type/class, ownership, and alliance with BPJSK, significantly influence medicines cost (p = 0.000). Patients in hospitals not allied with BPJSK are charged more than fourfold higher than the other group (mean IDR 4,892,570 vs. IDR 1,194,757). Patients' biological characteristics (sex and age) have no significant influence, unlike the length of stay, the number of diagnoses, and financial source. On average, the national health insurance (NHI) group pays less than a quarter (IDR 1,009,196) compared with the non-NHI group (IDR 4,261,870). Prescribing characteristics show a significant role except for injection percentage. The higher the percentage of generic and essential medicines prescribed, the lower the cost of the medicines is, while the increasing number of items also elevates medicines cost. Medicines cost for generic prescribing less than 50% is 4-5 times higher (mean = IDR 4,029,106) than the other groups. Encouraging the use of generic and essential medicines can reduce medical costs.