We report a 10-yr-old boy who developed CIPS after a second allogeneic BMT for severe aplastic anemia. He received the second BMT from the same HLA-matched sibling donor 16 months after the first BMT due to secondary graft failure. The preparative regimen for the second BMT consisted of fludarabine, cyclophosphamide, and anti-thymocyte globulin. Prophylaxis for acute GVHD was tacrolimus and oral PSL. Engraftment was achieved on day 15. On day 19, he suddenly complained of intermittent pain in the bilateral lower limbs. Electric shock-like pain continued for a few minutes in succession. This intractable pain was not ameliorated by various analgesic drugs including pentazocine. MRI demonstrated bone marrow edema with high T2 signal intensity in the femur. He was diagnosed as CIPS based on his symptoms and MRI findings. The trough concentration of tacrolimus (10.1 ng/mL) at the onset of CIPS was within the therapeutic range. Bouts of severe pain naturally resolved after day 43 without the discontinuation of tacrolimus. CIPS is a rare complication in HSCT. This is the first non-malignant, and the first pediatric, case who developed CIPS after HSCT.