The aim of this work was to understand between-hospital variation in thrombolysis use among emergency stroke admissions in England and Wales. A total of 88,928 patients who arrived at all 132 emergency stroke hospitals in England Wales within 4 h of stroke onset, from 2016 to 2018. Machine learning was applied to the Sentinel Stroke National Audit Programme (SSNAP) data set, to learn which patients in each hospital would likely receive thrombolysis. We used XGBoost machine learning models, coupled with a SHAP model for explainability; Shapley (SHAP) values, providing estimates of how patient features, and hospital identity, influence the odds of receiving thrombolysis. Thrombolysis use in patients arriving within 4 h of known or estimated stroke onset ranged 7% -49% between hospitals. The odds of receiving thrombolysis reduced 9-fold over the first 120 min of arrival-to-scan time, varied 30-fold with stroke severity, reduced 3-fold with estimated rather than precise stroke onset time, fell 6-fold with increasing pre-stroke disability, fell 4-fold with onset during sleep, fell 5-fold with use of anticoagulants, fell 2-fold between 80 and 110 years of age, reduced 3-fold between 120 and 240 min of onset-to-arrival time and varied 13-fold between hospitals. The majority of between-hospital variance was explained by the hospital, rather than the differences in local patient populations. Using explainable machine learning, we identified that the majority of the between-hospital variation in thrombolysis use in England and Wales may be explained by differences in in-hospital processes and differences in attitudes to judging suitability for thrombolysis.