The present report describes an incomplete atypical femoral fracture (AFF) patient who underwent simultaneous autogenous bone transplantation to the resected fracture region during intramedullary nail fixation. A 73-year-old female with a history of multiple myeloma had been undergoing treatment with intravenous drip injections of Zoledronic Acid. She was introduced to our department due to the left lateral thigh pain, with no trauma incidence. An anteroposterior radiograph showed a transverse thin fracture line with localized periosteal and endosteal thickening, which is compatible with subtrochanteric incomplete AFF. A biochemical investigation revealed the existence of severely suppressed bone turnover. She underwent intramedullary nail fixation for fear of a complete fracture. After the fixation, the cortical bone at the fracture region was excised as a wedge-shaped block, and bone marrow extracted from the hollow reamer was simultaneously transplanted to the resected fracture region. Histological examination showed few bone formation features at the fracture line in the excised lateral cortical bone. At 7 months after surgery, radiographs demonstrated complete bone repair, and no clinical problems were observed two years postoperatively. To the best of our knowledge, this is the first report in which autogenous bone marrow transplantation, noninvasive to the iliac crest, was performed in an incomplete AFF patient. We believe that this low invasive procedure can be a useful technique for AFF treatment.