Background: In acute infarction patients, small cortical cerebellar infarctions (SCCI) on MRI (assessed on diffusion-weighted imaging, with SCCI often chronic and asymptomatic) are associated with acute cardioembolic infarction. In young cryptogenic stroke patients, patent foramen ovale (PFO) is thought to be a potential source of cardioembolic infarction. We hypothesize that SCCI on MRI would be associated with PFO in young cryptogenic stroke patients. Methods: A total of 321 consecutive young (≤50 years) stroke patients admitted between January 2015 and July 2019 were screened. Of these patients, 287 patients had diagnostic work-up including early-phase MRI, intra- and extracranial vessel imaging, contrast transoesophageal or contrast transthoracic echocardiography, and ≥24 h ECG-monitoring. We retrospectively analyzed MRI scans of the 112 patients with cryptogenic stroke, including 63 with and 49 without PFO. Between both groups, we compared baseline characteristics (including cardiovascular risk factors and history of stroke), MRI characteristics of acute symptomatic infarction (cortical/subcortical localization, arterial territory, lesion number, and lesion size in case of subcortical infarction), atrial septum aneurysm (ASA) presence, and acute and chronic SCCI and non-SCCI lesions assessed on diffusion-weighted imaging. Results: Groups with and without PFO were comparable in regard to performed vessel imaging and echocardiography modalities, baseline characteristics, and acute infarction characteristics, except for more frequent current smoking (67 vs. 44%, p = 0.022) and multiterritorial infarction (14 vs. 0%, p = 0.0024) and less frequent ASA (10 vs. 48%, p < 0.001) in the group without PFO. Risk of Paradoxal Embolism score was >6 in 76% of patients with PFO. SCCI was more frequent in patients with than without PFO (33 vs. 10%, p = 0.0061; OR 4.4, 95% CI 1.5–12.7), with chronic and asymptomatic SCCI in the vast majority of cases. No difference was observed for non-SCCI lesions. Conclusions: Chronic SCCI are strongly associated with PFO in young cryptogenic stroke patients. Clinical Trial Registration-URL: http://www.clinicaltrials.gov. Unique identifier: NCT04043559.