Background Administrative data are frequently used in stroke research. Ensuring accurate identification of patients who had an ischaemic stroke, and those receiving thrombolysis and endovascular thrombectomy (EVT) is critical to ensure representativeness and generalisability. We examined differences in patient samples based on mode of identification, and propose a strategy for future patient and procedure identification in large administrative databases. Methods We used non-public administrative data from the state of California to identify all patients who had an ischaemic stroke discharged from an emergency department (ED) or inpatient hospitalisation from 2010 to 2017 based on International Classification of Disease (ICD-9) (2010-2015), ICD-10 (2015-2017) and Medicare Severity-Diagnosis-related Group (MS-DRG) discharge codes. We identified patients with interhospital transfers, patients receiving thrombolytics and patients treated with EVT based on ICD, Current Procedural Terminology (CPT) and MS-DRG codes. We determined what proportion of these transfers and procedures would have been identified with ICD versus MS-DRG discharge codes. Results Of 365 099 ischaemic stroke encounters, most (87.70%) had both a stroke-related ICD-9 or ICD-10 code and stroke-related MS-DRG code; 12.28% had only an ICD-9 or ICD-10 code and 0.02% had only an MS-DRG code. Nearly all transfers (99.99%) were identified using ICD codes. We identified 32 433 thrombolytic-treated patients (8.9% of total) using ICD, CPT and MS-DRG codes; the combination of ICD and CPT codes identified nearly all (98%). We identified 7691 patients treated with EVT (2.1% of total) using ICD and MS-DRG codes; both MS-DRG and ICD-9/ICD-10 codes were necessary because ICD codes alone missed 13.2% of EVTs. CPT codes only pertain to outpatient/ED patients and are not useful for EVT identification. Conclusions ICD-9/ICD-10 diagnosis codes capture nearly all ischaemic stroke encounters and transfers, while the combination of ICD-9/ICD-10 and CPT codes are adequate for identifying thrombolytic treatment in administrative datasets. However, MS-DRG codes are necessary in addition to ICD codes for identifying EVT, likely due to favourable reimbursement for EVT-related MS-DRG codes incentivising accurate coding.