Bacterial bloodstream infections (BSIs) are associated with poor outcomes following stem cell transplantation (SCT). We describe the demographics, treatment, complications, and outcome of 23 pediatric SCT recipients who developed three or more BSIs in the first year after SCT at our center from 2011 through 2016. The majority underwent allogeneic SCT (n = 22/23;96%), mainly from an unrelated donor (n = 19/22,86%); developed grade 2-4 graft versus host disease (GVHD; n = 14/23, 61%), all steroid refractory; and were diagnosed with thrombotic microangiopathy (n = 21/23, 91%). One-year overall survival was 56% (n = 13/23). We observed a high rate of transplant-associated thrombotic microangiopathy and steroid-refractory acute GVHD in patients with three or more BSIs.