Background: Acute infarction patterns have been described in cardioembolic stroke, mainly with atrial fibrillation (AF) or patent foramen ovale. We aimed to analyse acute infarction magnetic resonance imaging (MRI) characteristics in stroke patients with intracardiac thrombus (ICT) compared with stroke patients with AF. Methods: We performed a retrospective study analysing brain MRI scans of consecutive acute symptomatic cardioembolic infarction patients associated with ICT or AF who were recruited and registered in the stroke database between June 2018 and November 2019. Diffusion-weighted imaging performed within 1 week after symptom onset, intra-/extracranial vessel imaging, echocardiography, and ≥24-h ECG monitoring were required for inclusion. Baseline, biological, and echocardiography characteristics were assessed. Analysed MRI characteristics were infarction location (anterior/middle/posterior cerebral artery territory; anterior/posterior/mixed anterior-posterior circulation; multiterritorial infarction; brainstem; cerebellum; small cortical cerebellar infarctions [SCCIs] or non-SCCI; cortical/subcortical/cortico-subcortical), lesion number, subcortical lesion size (> or <15 mm), and total infarction volume. Results: We included 28 ICT and 94 AF patients presenting with acute stroke. ICT patients were younger (median age 66 vs. 81 years, p < 0.001), more frequently male (79 vs. 47%, p = 0.003), and smokers (39 vs. 17%, p = 0.013), had more frequent history of diabetes (36 vs. 18%, p = 0.049) and ischaemic heart disease (57 vs. 21%, p < 0.001), and had lower HDL cholesterol levels (0.39 vs. 0.53 g/L, p < 0.001). On MRI, SCCI was more frequent in the ICT group (25 vs. 5%, p = 0.006) in the absence of other differences in infarction localisation, number, size, or volume on MRI. On multivariate analysis, younger age (p < 0.001), history of ischaemic heart disease (p < 0.001), and low HDL cholesterol levels (p = 0.01) were significantly associated with ICT. Results approaching statistical significance were observed for SCCI (more frequent in the ICT group, p = 0.053) and non-SCCI (more frequent in the AF group, p = 0.053) on MRI. Conclusions: ICT-related stroke is associated with acute SCCI presence on MRI. Clinical Trial Registration-URL: http://www.clinicaltrials.gov. Unique identifier: NCT04456309.