The mortality rate associated with respiratory failure due to invasive fungal infections after allogeneic hematopoietic stem cell transplantation (HSCT) is exceedingly high. We present a retrospective analysis of 4 HSCT recipients who survived long-term artificial respiration subsequent to pulmonary mycosis, and compare our current findings with historic data. Several clinical parameters indicate a remarkable improvement in the clinical courses of those patients in recent years: weaning time, extubation rate, and improvement of additional organ failures were all significantly better in patients treated after the emergence of new antimycotic agents, resulting in prolonged overall survival. We propose that our observations reflect an improved management of these patients, mainly because of the use of new antimycotics with alternative mechanisms of action and decreased toxicity, allowing for earlier, more aggressive, and more effective antifungal treatment approaches. In addition, the optimized use of new technologies designed to augment spontaneous breathing efforts by patients, mechanical ventilation, as well as the advantages of early tracheotomy will contribute to better outcomes in the treatment of respiratory failure due to pulmonary mycoses following allogeneic HSCT.