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Objective: To analyze the effect of intraparotid injection of botulinum neurotoxin A (BoNT-A) on salivary production and the course of pharyngocutaneous fistula (PCF) in post-radiation therapy salvage surgery. Methods: A total of 13 patients who had undergone total laryngectomy or pharyngolaryngectomy were treated with BoNT-A to both parotid glands, within three days from PCF onset. The salivary flow was evaluated using a subjective rating scale as the percentage of normal function from 0% (no saliva) to 100% (normal saliva flow), before injection, every day for 2 weeks, and once a week for three months. PCFs were monitored daily. Results: Spontaneous closure of PCF occurred in 7/13 (53.84%) cases 13.6 days (range: 7–18) after treatment; 6/13 (46.16%) patients needed revision surgery. Salivary flow significantly decreased in all patients seven days after injection (from 67.2% to 36.4%; p < 0.05). Patients who had undergone either conservative or surgical treatment did not differ in salivary flow before injection, whereas the mean percentages of salivary flow calculated at each time point after injection were different (p < 0.05). Conclusions: BoNT-A contributed to the closure of the fistula in most of our cases. The subjective perception of salivary flow predicted the closure of PCF. The mean time to closure may contribute to establishing the timing of PCF surgical treatment.