We describe a 4-year-old-girl with familial hemophagocytic lymphohistiocytosis (FHL) who developed disseminated cutaneous nontuberculous mycobacterial (NTM) infection after unrelated cord blood stem cell transplantation (uCBSCT). After transplantation, the patient developed steroid-refractory acute graft-versus-host disease, and was given methylprednisolone, cyclosporin and mycophenolate mofetil. Six months after uCBSCT, cutaneous lesions that looked like insect bites appeared and spread widely over the thighs. NTM infection was diagnosed by skin biopsy although no organism could be identified. Minocycline (MINO) and sulfamethoxazole/trimethoprim (ST) were administered. However, the cutaneous disease followed a course of remissions and exacerbations. One month after the skin biopsy, mycobacterium chelonae was detected by bacteriological culture of abscess drainage. Ten months after uCBSCT, the cutaneous lesions quickly progressed and the inguinal lymph nodes became enlarged and painful. Then the antibiotics were switched from MINO and ST to amikacin and clarithromycin (CAM) based on the results of mycobacterial susceptibility test. The cutaneous lesions gradually improved after continuous administration of CAM. Cutaneous NTM infection is rare, but it may occur in immunocompromised patients after SCT.