It is unknown whether heart failure (HF) with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF) carry a similar risk of stroke or systemic embolism (SE) and other outcomes in patients with nonvalvular atrial fibrillation (AF). A prospective, multicenter outpatient registry with echocardiographic data which enrolled 10,589 patients from June 2016 to May 2019 was analyzed. In this registry, 935 (8.8%) patients had HF, and the proportions of patients with HFpEF and HFrEF were 43.2% and 56.8%, respectively. During follow-up over 1.33 years, 11 (2.07 per 100 person-years [PYR]) and 5 (0.76 per 100 PYR) patients had stroke/SE in the HFpEF and HFrEF groups, respectively, whereas 102 patients (0.84 per 100 PYR) had these sequelae in the no-HF group. The HFpEF group had a significantly higher cumulative incidence of stroke/SE (p = 0.004) and risk of stroke/SE (adjusted hazard ratio [HR] 2.23, 95% confidence interval [CI] 1.19 to 4.18) than the no-HF group. The risk of stroke/SE in the HFpEF group compared with that in the no-HF group was consistently increased even in patients on oral anticoagulation therapy (adjusted HR 2.55, 95% CI 1.31 to 4.96). There was a correlation between larger left atrial size and risk of stroke/SE (adjusted HR 1.53, 95% CI 1.03 to 2.29), but not between reduced left ventricular ejection fraction and this risk. In conclusion, these results suggest that strict oral anticoagulation therapy helps reduce the risk of stroke/SE in patients with nonvalvular AF and HFpEF, especially in those with a larger left atrial size.