Background: Currently, there are no recommendations regarding the use of heparinized flush during endovascular thrombectomy (EVT) for acute ischemic stroke. Periprocedural heparin could, however, affect functional outcome and symptomatic intracranial hemorrhage (sICH). We surveyed protocols on heparin flush concentrations in Dutch EVT centers and assessed its effect on safety and efficacy outcomes. Methods: Patients registered in the MR CLEAN Registry, from 2014 up to 2017 were included. We collected data on center protocols regarding heparin flush concentrations (IU/L) and grouped patients by their per protocol administered heparin flush concentration. We used a random effects model with random intercepts by EVT center and analyzed endpoints using regression models. Endpoints were sICH, mRS at 90 days, mortality and reperfusion rates. Results: A total of 3157 patients were included of which 45% (6 centers) received no heparin in the flush fluids, 1.8% (1 center) received flush fluids containing 2000 IU/L heparin, 26% (4 centers) received 5000 IU/L, 22% (4 centers) received 10.000 IU/L and 5.6% (1 center) received 25.000 IU/L. Higher heparin concentration was associated with increased sICH (aOR 1.15; 95% CI 1.02–1.29), but not with functional outcome, mortality or reperfusion rates. Conclusion: Effect of heparin in flush fluids should not be ignored by clinicians or researchers as higher concentrations may be associated with higher rates of ICH. The observed variation in protocols regarding heparin concentrations between EVT centers should encourage further studies, ideally in a controlled way, resulting in recommendations on heparin use in flush fluids in future guidelines.