The investigation of the potential association between ischemic stroke and subclinical atrial fibrillation (SCAF) is important for secondary prevention. We aimed to determine whether SCAF can be predicted by atrial substrate measurement with P wave signal-averaged electrocardiography (SAECG). We recruited 125 consecutive patients with embolic stroke of undetermined source (ESUS) and 125 patients with paroxysmal atrial fibrillation as controls. All participants underwent P wave SAECG at baseline, and patients with ESUS were followed up with Holter monitoring and electrocardiography at baseline, 3, 6, and 12 months after discharge and every 6 months thereafter. In the ESUS group, 32 (25.6%) patients were diagnosed with SCAF during follow-up. There were no significant differences between the groups regarding atrial substrate. P wave duration (PWD) was a significant predictor of SCAF. Stroke recurrence occurred in 22 patients (17.6%), and prolonged PWD (≥ 135 ms) predicted stroke recurrence more robustly than SCAF detection. In ESUS patients, PWD can be a useful biomarker to predict SCAF and to identify patients who are more likely to have a recurrent embolic stroke associated with an atrial cardiopathy. Further research is needed for supporting the utility and applicability of PWD.