The number of patients with nonvalvular atrial fibrillation (NV-AF) who require long-term anticoagulation and also have a higher risk of bleeding is increasing. Recently, there is no information regarding real on-treatment anti-Xa activity in patients with NV-AF and a higher risk of bleeding who receive oral factor Xa inhibitors. The aim of this study was to determine trough and peak anti-Xa activity in these patients. This single-centre pilot study enrolled 41 patients with NV-AF and a higher risk of bleeding defined as Hypertension, Abnormal Renal/Liver Function, Stroke, Bleeding History or Predisposition, Labile INR, Elderly, Drugs/Alcohol Concomitantly score at least 3 points. Twenty-one patients were treated with rivaroxaban and 17 patients were treated with apixaban. The trough and peak samples of these patients were tested for anti-Xa activity with factor Xa-calibrated anti-Xa chromogenic analysis. The detected trough anti-Xa activity was 63.2 ± 44.4 ng/ml. There was a significant increase in peak anti-Xa activity up to 170.3 ± 99.6 ng/ml (P < 0.001) observed. There were no significant differences in trough (52.4 ± 41.9 vs. 76.0 ± 45.4 ng/ml; P = 0.12) and peak (187.2 ± 122.5 vs. 151.5 ± 64.0 ng/ml; P = 0.27) anti-Xa activity between rivaroxaban-treated and apixaban-treated patients. This study demonstrated the anti-Xa activity in oral factor Xa inhibitor-treated patients with NV-AF and a higher risk of bleeding. No significant differences in this activity between rivaroxaban-treated and apixaban-treated patients were found.