Currently, data on the effects of the novel Coronavirus disease (COVID-19) on hematopoietic stem cell transplant (HSCT) recipients is limited. In this case, an 8-year-old male with IPEX syndrome underwent allogeneic HSCT and was found COVID-19 positive 23 days post-transplant. He was treated with a 10-day course of remdesivir, three doses of tocilizumab, and two units of COVID-19 convalescent plasma (CCP). Initially, inflammatory markers decreased with treatment. However, he experienced primary graft failure, most likely secondary to COVID-19 infection, developed multiple systemic infections, and subsequently died before a second graft infusion could be administered.