Allogeneic haematopoietic cell transplantation (HCT) remains the only treatment that can correct the haematological manifestations in patients with Fanconi anaemia. Over the last two decades, sequential changes to the approach to HCT have resulted in reduced regimen-related toxicity, superior engraftment and less graft-versus-host disease (GVHD), resulting in improved survival. The two pivotal changes that most influenced these improvements were the addition of fludarabine to the preparative regimen to augment engraftment, and the use of T cell depletion to reduce GVHD. With these improved HCT outcomes, indications for HCT are quite consistent regardless of donor source. Emphasis is now being placed on developing HCT regimens that will improve quality of life by reducing late effects, particularly the risk of malignancy, sterility and endocrinopathies. This paper will review the unique challenges of HCT in FA patients, with particular emphasis on the timing and approach to HCT.