We report a rare case of first and second branchial arch syndrome with fistula originated from the first pharyngeal pouch. A 10-day-old female was referred to our clinic with a complaint of left microtia with fistula at the mandibular angle. On preoperative examinations, X-ray with angiography flexible wire inserted into the fistula and computed tomography with contrast enhancement of the fistula revealed that the fistula was connected to the middle ear cavity. Fistulectomy was performed at the age of 7. Pathological examinations demonstrated that the fistula consisted of a single layer of cylindrical epithelium, suggesting that it originated from the endoderm. Based on surgical, imaging, and pathological findings, the fistula originated from first pharyngeal pouch. Preoperative X-ray with angiography flexible wire inserted into the fistula and the computed tomography with contrast enhancement of the fistula were useful for planning operation.