The aim of this study was to develop a convolutional neural network (CNN) that automatically detects and segments intra-arterial thrombi on baseline non-contrast computed tomography (NCCT) scans. We retrospectively collected computed tomography (CT)-scans of patients with an anterior circulation large vessel occlusion (LVO) from the Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands trial, both for training (n = 86) and validation (n = 43). For testing we included patients with (n = 58) and without (n = 45) an LVO from our comprehensive stroke center. Ground truth was established by consensus between two experts using both CT angiography and NCCT. We evaluated the CNN for correct identification of a thrombus, its location and thrombus segmentation and compared these with the results of a neurologist in training and expert neuroradiologist. Sensitivity of the CNN thrombus detection was 0.86, vs. 0.95 and 0.79 for the neuroradiologists. Specificity was 0.65 for the network vs. 0.58 and 0.82 for the neuroradiologists. The CNN correctly identified the location of the thrombus in 79% of the cases, compared to 81% and 77% for the neuroradiologists. The sensitivity and specificity for thrombus identification and the rate for correct thrombus location assessment by the CNN were similar to those of expert neuroradiologists.