Fusarium species, a soil-borne fungi, causes disease in animals and humans, particularly in immunocompromized patients. A 62-year-old male presented with type II diabetes mellitus, diagnosed 4 years ago. He had a motorcycle accident-caused open tibiofibular fracture of the left lower extremity (Gustilo grade IIIb). With open reduction and internal fixation, an anterolateral thigh musculocutaneous flap was harvested for coverage of exposed bone and defect reconstruction. Partial failure of the flap occurred 9 days following reconstruction, and histological examination revealed Fusarium spp. After treatment with antifungal drugs and debridement, we performed a split-thickness skin graft. At 2-year follow-up, the flap was viable with adequate bone union. This is the first reported case of partial flap failure due to a Fusarium spp. infection. Possibility of fungal infections in patients with late-onset flap failure should be noted. Prompt diagnosis and treatment are needed to prevent repeated free-tissue transfer and/or devastating outcomes.