Background A pharyngocutaneous fistula is a common and difficult-to-manage complication after head and neck reconstruction. It can lead to serious complications such as flap failure, carotid artery rupture, and pharyngeal stricture, and may require additional surgery. Previous radiotherapy, a low serum albumin level, and a higher T stage have been proposed as contributing factors. We aimed to clarify the risk factors for pharyngocutaneous fistula in patients who underwent flap reconstruction and to describe our experiences in treating pharyngocutaneous fistula. Methods Squamous cell carcinoma cases that underwent flap reconstruction after cancer resection from 1995 to 2013 were analyzed retrospectively. We investigated several significant clinical risk factors. The treatment modality was selected according to the size of the fistula and the state of the surrounding tissue, with options including conservative management, direct closure, flap surgery, and pharyngostoma formation. Results A total of 127 cases (18 with fistulae) were analyzed. A higher T stage (P=0.048) and tube-type reconstruction (P=0.007) increased fistula incidence; other factors did not show statistical significance (P>0.05). Two cases were treated with conservative management, 1 case with direct closure, 4 cases with immediate reconstruction using a pectoralis major musculocutaneous flap, and 11 cases with direct closure (4 cases) or additional flap surgery (7 cases) after pharyngostoma formation. Conclusions Pharyngocutaneous fistula requires global management from prevention to treatment. In cases of advanced-stage cancer and tube-type reconstruction, a more cautious approach should be employed. Once it occurs, an accurate diagnosis of the fistula and a thorough assessment of the surrounding tissue are necessary, and aggressive treatment should be implemented in order to ensure satisfactory long-term results.