Immune tolerance induction (ITI) in haemophilia B patients with inhibitor should be carefully considered because of the relatively poor (25%) overall success rate and the high risk of complications. ITI in combination with an immunosuppressive treatment was started in two children with haemophilia B with factor IX (FIX) inhibitor. To avoid anaphylactic reactions and inhibitor boost, the FIX replacement therapy was stopped and patients received a treatment with recombinant activated factor VII (rFVIIa). After disappearance of FIX inhibitor, a combination of mycophenolate-mofetil (MMF), dexamethasone (DEXA) and intravenous immunoglobulin (IVIG) and a high dose FIX replacement therapy was started. Immune tolerance could be induced in patient 2, whereas eradication of FIX inhibitor was incomplete in patient 1. Both patients benefited from the immune suppressive treatment and FIX replacement therapy was tolerated without any allergic complications. Neither development of a nephrotic syndrome nor a severe bleeding episode was observed. Strategies to induce tolerance in haemophilia B patients with inhibitors need to be explored in a systematic way. Given the low frequency of disease and even lower incidence of inhibitors, prospective randomized studies may not be possible. International registry-based retrospective and prospective data collection could play the key role in the study of the outcome variables in ITI for haemophilia B.