Risk for thrombotic events with factor IX replacement therapy in patients with haemophilia B remains a concern for patients, those who treat them, and regulatory agencies, based on experience with early use of prothrombin complex concentrates. The current post hoc analysis assessed the incidence of thrombotic events and changes in prothrombin fragment 1 + 2, thrombin–antithrombin complex, and D-dimer in 221 patients with haemophilia B who received nonacog alfa in clinical studies. Thrombotic event and coagulation marker data were collected from 8 interventional studies utilizing on-demand, prophylactic, and preventive regimens in patients with haemophilia B. Mean age was 25 years (min–max, 0–69), with 51 (23%) patients aged less than 12 years and 15 (7%) aged less than 2 years. None tested positive for inhibitors. Mean time on study was 60.9 ± 32 weeks and mean number of exposure days was 69.3 (min–max, 1–496). Sixty-nine (31%) patients regularly received infusions that were approximately 100 IU/kg as part of a routine prophylaxis regimen, and 29 (13%) patients underwent surgical procedures. No clinical thrombotic events were reported, and no patient experienced clinically significant changes in coagulation markers between baseline and end-of-study testing. These collective data support the low thrombotic risk associated with nonacog alfa in paediatric, adult, and surgical patients with haemophilia B receiving different treatment regimens, including doses of approximately 100 IU/kg. Although careful thrombotic clinical evaluation is important, regular coagulation marker monitoring does not appear to be warranted in patients with haemophilia B.