The emergence of new antifungal compounds with alternative mechanisms of action and improved tolerability has opened up new therapeutic possibilities for the use of combined antifungal treatment in life-threatening systemic fungal infections. A case report of an 8-year-old allogeneic stem cell transplant recipient who developed a central venous catheter tunnel infection caused by Aspergillus flavus is presented here. In spite of conventional and subsequent liposomal amphotericin B therapy the infection progressed rapidly and the necrosis extended further to the thoracic wall, pleura and the right lung. Combined treatment consisting of liposomal amphotericin B and caspofungin was instituted. After 30 days of dual therapy the deep fungal infection resolved and the extensive soft tissue defect showed scarring. One year post-transplant, the patient is well, with normal bone marrow function and full donor chimerism. Although there is limited clinical data on the effectiveness of echinocandins in pediatric patients with documented invasive fungal infections, this case report shows that combining liposomal amphotericin B with caspofungin could be advantageous.