Background and objective Computed tomography perfusion (CTP) is widely used in the evaluation of acute ischemic stroke patients for endovascular thrombectomy (EVT). The stability of CTP core estimation is suboptimal and varies between software packages. We aimed to quantify the volumetric and spatial agreement between the CTP ischemic core and follow-up infarct for four ischemic core estimation approaches using syngo.via. Methods We included successfully reperfused, EVT-treated patients with baseline CTP and 24h follow-up diffusion weighted magnetic resonance imaging (DWI) (November 2017–September 2020). Data were processed with syngo.via VB40 using four core estimation approaches based on: cerebral blood volume (CBV)<1.2mL/100mL with and without smoothing filter, relative cerebral blood flow (rCBF)<30%, and rCBF<20%. The follow-up infarct was segmented on DWI. Results In 59 patients, median estimated CTP core volumes for four core estimation approaches ranged from 12–39 mL. Median 24h follow-up DWI infarct volume was 11 mL. The intraclass correlation coefficient (ICC) showed moderate–good volumetric agreement for all approaches (range 0.61–0.76). Median Dice was low for all approaches (range 0.16–0.21). CTP core overestimation >10mL occurred least frequent (14/59 [24%] patients) using the CBV-based core estimation approach with smoothing filter. Conclusions In successfully reperfused patients who underwent EVT, syngo.via CTP ischemic core estimation showed moderate volumetric and spatial agreement with the follow-up infarct on DWI. In patients with complete reperfusion after EVT, the volumetric agreement was excellent. A CTP core estimation approach based on CBV<1.2 mL/100mL with smoothing filter least often overestimated the follow-up infarct volume and is therefore preferred for clinical decision making using syngo.via.