We describe a case of fatal acute disseminated breakthrough toxoplasmosis in a 19-year-old adolescent after haploidentical hematopoietic stem cell transplantation for acute lymphoblastic leukemia despite continued atovaquone prophylaxis. Diagnosis was at necropsy, and confirmed by postmortem polymerase chain reaction analysis in plasma. This report illustrates the need for protozoal monitoring despite atovaquone prophylaxis, in severely immunocompromised patients with intolerance to standard treatment.