Objectives The aim of the present study was to determine the direct medical costs of hospitalisations for ischaemic stroke (IS) in-patients with different types of health insurance in China and to analyse the demographic characteristics of hospitalised patients, based on data supplied by the China Health Insurance Research Association (CHIRA). Methods A nationwide and cross-sectional sample of IS in-patients with International Classifications of Diseases 10th Revision (ICD-10) Code I63 who were ensured under either the Basic Medical Insurance Scheme for Employees (BMISE) or the Basic Medical Insurance Scheme for Urban Residents (BMISUR) was extracted from the CHIRA claims database. A retrospective analysis was used with regard to patient demographics, total hospital charges and costs. Results Of the 49588 hospitalised patients who had been diagnosed with IS in the CHIRA claims database, 28850 (58.2%) were men (mean age 67.34 years) and 20738 (41.8%) were women (mean age 69.75 years). Of all patients, 40347 (81.4%) were insured by the BMISE, whereas 8724 (17.6%) were insured by the BMISUR; the mean age of these groups was 68.55 and 67.62 years respectively. For BMISE-insured in-patients, the cost per hospitalisation was RMB10131 (95% confidence interval (CI) 10014-10258), the cost per hospital day was RMB787 (95% CI 766-808), the out-of-pocket costs per patient were RMB2346 (95% CI 2303-2388) and the reimbursement rate was 74.61% (95% CI 74.48-74.73%). For BMISUR-insured in-patients the cost per hospitalisation was RMB7662 (95% CI 7473-7852), the cost per hospital day was RMB744 (95% CI 706-781), the out-of-pocket costs per patient were RMB3356 (95% CI 3258-3454) and the reimbursement rate was 56.46% (95% CI 56.08-56.84%). Conclusions Costs per hospitalisation, costs per hospital day and the reimbursement rate were higher for BMISE- than BMISUR-insured in-patients, but BMISE-insured patients had lower out-of-pocket costs. The financial burden was higher for BMISUR- than BMISE-insured in-patients. For BMISUR-insured in-patients, the out-of-pocket payment was 43.54% of total expenses, which means the government should increase the financial investment, raise reimbursement rates and set up differential reimbursements to meet the health needs of in-patients with different income levels. What is known about the topic? Cardiovascular and cerebrovascular diseases are major non-communicable diseases affecting the health of the Chinese population. The China Health Statistics Yearbook (2013) reported that across all in-patients, 195million (5.82%) had been discharged with a diagnosis of cerebrovascular disease. Of these, 118million had IS, accounting for 60.51% of all in-patients with cerebrovascular disease and 54.97% of hospitalisation costs for all cerebrovascular disease in-patients. After the two basic insurance systems, namely the BMISE and BMISUR, had been established, the out-of-pocket expenses for patients were reduced. However, to date there have been no studies investigating how the different types of health insurance (i.e. the BMISE and the BMISUR) affected the costs of treatment of IS in-patients in China. What does this paper add? This paper reports the direct costs for patients diagnosed with IS based on data supplied by the CHIRA. Direct hospitalisation costs depending on the type of insurance cover, age and gender were also evaluated. What are the implications for practitioners? The present study found that the personal financial burden of disease treatment was higher for in-patients insured under the BMISUR than BMISE. For in-patients insured under the BMISUR, the out-of-pocket payment was 43.54% of total expenses, which means the government should increase the financial investment, raise reimbursement rates and set up differential reimbursement rates to meet the health needs of patients with different incomes.