In free jejunum transfer, knowing the ischemic tolerance time of the jejunum is crucial. It helps determine the need for reharvesting if an unexpected situation prolongs the ischemic time. The current ischemic tolerance time in humans is unknown. We investigated the relationship between ischemic time and postoperative complications in head and neck cancer patients who underwent free jejunum transfer. The study included 76 patients with available medical records out of 103 patients who underwent free jejunum transfer between 2009 and 2023. The association between the surgical procedure, including ischemic time, and patient's background, and flap engraftment, stenosis of the intestinal anastomosis, the swallowing function, and other complications was investigated. The ischemic time for jejunal flaps ranged from 1 h 24 min to 6 h, with a mean of 197 ± 55.5 min. In 72 patients, the jejunum was successfully engrafted, but vascular occlusion occurred in another four patients. In three of these patients, jejunal necrosis occurred, and there was no specific trend in ischemic time. Stenosis of the intestinal anastomosis occurred in 17 cases (22%), with ischemic time (≥3 h) and age (≥75 years) being significant factors for stenosis (ischemic time: 30% vs. 10%, p = 0.048, age: 50% vs. 15%, p < 0.01). No significant correlations were observed with other complications or the swallowing function. There was no specific trend between ischemic time and jejunal survival rate, indicating that an ischemic time within 6 h may not have affected engraftment. Although we have recently performed intestinal anastomosis prior to vascular anastomosis, the choice of surgical technique should be adapted to the patient's age and background.