A 17-month-old Japanese Black cow presented with inappetence, wheezing, dysphagia, and drooling. Radiography and ultrasonography revealed an oval, dorsal, pharyngeal mass, with an internal horizontal line demarcating the radiolucent area from the radio-opaque area. Upper airway endoscopy revealed pus-like deposits in the dorsal nasal passage, hyperemia, and edema in the dorsal pharynx, leading to swelling and airway obstruction. Manual palpation, after sedation, revealed a thickened mass surface, which was difficult to rupture with manual pressure. After inserting a linear sonographic probe through the mouth to establish the vascularity surrounding the mass and to identify a relatively thin-walled area, a trocar was pierced into the mass under endoscopic guidance, and the opening was enlarged manually. The mass was filled with stale pus-like material, which was removed manually. The abscess cavity was washed using saline and povidone–iodine. Day 1 post-surgery, dysphagia and wheezing disappeared. Day 16 post-surgery, endoscopy showed significant improvement in the airway patency. One year postoperatively, the owner reported that the cow had an uneventful recovery. For deep abscesses, such as bovine pharyngeal abscesses, it is important to perform a preoperative transoral Doppler ultrasonography to assess the vascularity and thickness of the abscess wall for safe trocar insertion and abscess drainage.