Background: In the general population, carotid intima-media thickness (CIMT) is associated with atherosclerosis as well as atrial fibrillation (AF). However, the extent to which CIMT might be of diagnostic value in clarifying stroke etiology is currently unclear. Methods: In this retrospective cohort study, we included 800 consecutive patients with acute ischemic stroke. We compared CIMT-values between stroke etiologies. The association between CIMT and cardioembolic stroke was investigated via logistic regression analysis adjusting for vascular risk factors. Receiver operating characteristic analyses were conducted to investigate the diagnostic value of CIMT in comparison to vascular risk factors and clinical AF risk scores (CHA₂DS₂VASc, HAVOC, and AS5F). Results: CIMT-values were highest in patients with cardioembolic or atherosclerotic stroke origin. CIMT was associated with newly diagnosed AF compared against cryptogenic strokes (crude odds ratio (OR) per 0.1 mm-increase of CIMT: 1.26 (95% confidence interval (CI): 1.13–1.41)). After adjustment for vascular risk factors, the effect of CIMT on AF-diagnosis, however, was weakened (adjusted OR: 1.10 (95% CI: 0.97–1.25)). The diagnostic value of CIMT for detection of AF (AUC: 0.60, 95% CI: 0.54–0.65) was outperformed by AF risk scores. Among the scores investigated, the AS5F-score yielded best accuracy and calibration to predict newly diagnosed AF (AUC: 0.71, 95% CI: 0.65–0.78). Conclusions: CIMT may help in the diagnosis of stroke etiology. However, compared with vascular risk factors or clinical AF risk scores, CIMT does not provide substantial additional information on the risk of newly detected AF. Thus, stratification of AF risk based on scores, such as the AS5F, is advisable.