Scalp reconstruction, particularly with complex defects and infection risks, often favors microvascular free flaps. However, this method can result in unavoidable alopecia and undesirable aesthetics. This report describes a novel case where hair transplantation via follicular unit extraction (FUE) was applied to a free myocutaneous flap. A 44-year-old woman with Moyamoya disease suffered intracerebral hemorrhage a decade ago. Craniotomies and autologous bone cranioplasties led to wound dehiscence, with subsequent failed local flaps and skin grafts, and identification of a methicillin-resistant Staphylococcus aureus infection. The final scalp defect, measuring 13 × 9 cm, was reconstructed using a free myocutaneous latissimus dorsi flap. Nine years post-surgery, a 1,500-unit FUE hair transplantation procedure was conducted. The transplanted hair exhibited robust survival with adequate blood supply, achieving a satisfactory 80 to 85% survival rate at 12 months. This resulted in a notable improvement in the patient's external alopecia, with reported high levels of satisfaction. Free flaps offer a valuable method for scalp defect reconstruction; however, they may not ensure optimal aesthetic satisfaction due to alopecia. Nonetheless, successful FUE hair transplantation on a myocutaneous free flap can yield satisfactory aesthetic results.