The aim was to evaluate Virtual Non-Contrast (VNC)-CT images for the detection of acute infarcts in the brain after mechanical thrombectomy using a dual-layer spectral CT. 29 patients between September 2016 and February 2017 with unenhanced head spectral-CT after mechanical thrombectomy and available follow-up images (MRI, n:26; CT, n:3) were included. VNC-CT and conventional CT (CT) images were reconstructed using dedicated software. Based on those, contrast-to-noise ratio (CNR), and the volume of infarction were measured semi-automatically in VNC-CT, CT and MRI. Furthermore, two readers independently assessed the VNC-CT and CT images in a randomized order by using the ASPECT score, and inter-rater reliability, sensitivity and specificity were calculated. CNR was significantly higher in VNC-CT compared to CT (3.1 ± 1.5 versus 1.1 ± 1.1, p < 0.001). The mean estimated volume of infarction was significantly higher in VNC-CT compared to CT (72% versus 55% of the volume measured in MRI, p < 0.005). Inter-rater reliability was higher in VNC-CT compared to CT (0.751 versus 0.625) and sensitivity was higher in VNC-CT compared to CT (73% versus 55%). In conclusion, acute ischemic lesions after mechanical thrombectomy are better definable in VNC-CT compared to CT images using a dual-layer spectral CT system.