Paediatric haematopoietic cell transplantation has experienced significant advances in the last few decades. However, pulmonary complications are an important limitation to the efficacy of this intervention, contributing to post-transplantation morbidity and mortality. Such complications persist even in experienced centres and occur in adult and paediatric recipients. This review identifies the paediatric pulmonary complications that are commonly seen following haematopoietic cell transplantation and addresses both infectious and non-infectious aetiologies and their clinical manifestations, evaluation, and potential therapy. Ultimately, improvement in outcomes will require attention to immunosuppression as well as traditional diagnostic procedures and treatment. This article aims to review the current state of pulmonary complications post-transplantation, to examine the impact of our recent advances and changes in treatment, and to identify potential future therapies and hypothesise what role these might have on long-term survival.