X-linked chronic granulomatous disease (X-CGD) may be associated with McLeod syndrome (MLS) as a contiguous gene deletion syndrome. MLS is characterized by the loss of XK protein together with Kx antigen on red blood cell (RBC) surfaces and late-onset neurocognitive symptoms. X-CGD treatment involves hematopoietic cell transplantation (HCT), and severe hemolysis may occur due to Kx antigen sensitization. Here, we report successful HCT in a 7-year-old male with X-CGD and MLS achieved by depleting RBCs from the graft and adding rituximab to the conditioning regimen. No hemolytic events occurred, and he is doing well 2 years after HCT.