Despite the rare incidence, occult chronic thrombosis of peroneal veins of the fibula graft during the flap harvest presents a challenge to produce a successful reconstruction. In this article, we present a case of a 54-year-old man with chronic thrombosis of peroneal veins found during the harvest of the free fibula osteocutaneous flap for reconstruction of the mandible defect after tumor ablation. With near-total obliteration of the lumens, a small lumen with residual blood outflow was identified under microscopic magnification. A successful flap transfer was made possible by using the recanalized lumen around the chronic thrombus of the vein for microanastomosis. The pathological analysis of the vein revealed that the recanalized lumens and the endothelial cells–specific CD31 immunohistochemical stain highlighted the endothelium of regenerative lumen around the chronic thrombus. The abundant deposition of thick collagen fibers also suggested a chronic nature of the thrombus. However, although a successful microsurgical free osteocutaneous flap transfer might be possible in the patient with lower-limb chronic peroneal vein thrombosis, a careful preoperative evaluation with imaging study is recommended for high-risk patients.