Background: Cardiac thrombi are a major risk factor for ischemic stroke, but are rarely diagnosed in the acute phase. We examined characteristics and functional outcome of patients with ischemic stroke and a concomitant cardiac thrombus detected on cardiac CT performed in the acute phase. Patients and Methods: We used data from “Mind the Heart,” a prospective cohort study in which consecutive adult patients with acute ischemic stroke underwent prospective ECG-gated cardiac CT during their acute stroke imaging protocol. We compared characteristics, functional outcome (modified Rankin scale) and stroke recurrence rate at 90 days of patients with a cardiac thrombus on CT (defined as filling defect <100 Hounsfield Units) to those without a cardiac thrombus. Results: Among 452 included patients, cardiac CT detected 41 thrombi in 38 (8%) patients. Thrombi were most often located in the left atrial appendage (31/38 [82%]). Patients with a cardiac thrombus more frequently had intracranial occlusions in multiple vascular territories (5% vs 0.5%, p = 0.04) and a higher baseline NIHSS score (17 [IQR 6–22] vs 5 [IQR 2–3], p < 0.001) compared to patients without a cardiac thrombus. In 13/38 (34%) patients with a cardiac thrombus, no atrial fibrillation was detected. A cardiac thrombus was associated with worse functional outcome (adjusted common odds ratio 3.18 95%CI 1.68–6.00). Recurrence rate was not significantly different (8% vs 4%, aOR 1.50 (0.39–5.82). Discussion and Conclusion: Cardiac CT detected a cardiac thrombus in one in every 12 patients with acute ischemic stroke, and these patients had more severe deficits, multivessel occlusions, and a worse functional outcome.