Background and purpose: CT perfusion (CTP) might support decision making in patients with acute ischemic stroke by providing perfusion maps of ischemic tissue. Currently, the reliability of CTP is hampered by varying results between different post-processing software packages. The purpose of this study is to compare ischemic core volumes estimated by IntelliSpace Portal (ISP) and syngo.via with core volumes as estimated by RAPID. Methods: Thirty-five CTP datasets from patients in the MR CLEAN trial were post-processed. Core volumes were estimated with ISP using default settings and with syngo.via using three different settings: default settings (method A); additional smoothing filter (method B); and adjusted settings (method C). The results were compared with RAPID. Agreement between methods was assessed using Bland-Altman analysis and intraclass correlation coefficient (ICC). Accuracy for detecting volumes up to 25 mL, 50 mL, and 70 mL was assessed. Final infarct volumes were determined on follow-up non-contrast CT. Results: Median core volume was 50 mL with ISP, 41 mL with syngo.via method A, 20 mL with method B, 36 mL with method C, and 11 mL with RAPID. Agreement ranged from poor (ISP: ICC 0.41; method A: ICC 0.23) to good (method B: ICC 0.83; method C: ICC 0.85). The bias (1.8 mL) and limits of agreement (-27, 31 mL) were the smallest with syngo.via with additional smoothing (method B). Agreement for detecting core volumes ≤25 mL with ISP was 54% and 57%, 85% and 74% for syngo.via methods A, B, and C, respectively. Conclusion: Best agreement with RAPID software is provided by syngo.via default settings with additional smoothing. Moreover, this method has the highest agreement in categorizing patients with small core volumes.