Abstract Objective: Pharyngocutaneous fistula is one of the severe complications related to head and neck surgeries. Detecting the accurate three-dimensional location of both the fistula and leakage is essential for surgical treatment. Videofluoroscopy is usually used for locating these; however, its imaging is two-dimensional. We evaluated pharyngeal leakage and fistulae using Cone Beam Computed Tomography (CBCT), known for its three-dimensional high spatial resolution imaging, taken in a sitting position, with oral contrast (contrast CBCT). Methods: Pharyngeal leakage and fistulae were evaluated in a total of 31 subjects by sequentially performing videofluoroscopy and contrast CBCT. The detection accuracy of videofluoroscopy and contrast CBCT for leakage and fistula, as well as the ability to determine the extent and depth for surgical planning, were investigated and compared. Results: Videofluoroscopy and contrast CBCT showed suspicious leakage and/or fistula in six and three of the 31 subjects, respectively. Surgical findings revealed the presence of leakage and/or fistula in three of the 31 subjects. The positive predictive values of videofluoroscopy and contrast CBCT were 50% (3/6) and 100% (3/3), respectively. Contrast CBCT provided more precise images, showing the extent and depth of leakage and fistula in three-dimensions. Conclusion: The present study’s results indicate the usefulness of contrast CBCT in terms of accurate diagnosis of leakage and fistula, due to its three-dimensional imaging being performed with the patient in a sitting position. Level of evidence: 4.