Percutaneous tracheostomy insertion is commonly performed in the critical care setting. However, its applicability and safety in head and neck (H&N) surgery remains uncertain. This study aimed to compare complications and postoperative recovery for percutaneous tracheostomy versus surgical tracheostomy in H&N surgery. A total of 66 patients undergoing percutaneous tracheostomy as part of H&N microvascular surgery were identified retrospectively. A control cohort of 70 consecutive surgical tracheostomy cases performed by another surgical team in the same department was similarly determined. Generally, the complication rates in the percutaneous and surgical tracheostomy groups were similar, with overall rates being 42% and 31%, respectively. The percutaneous group experienced a higher rate of airway obstruction (15%), primarily due to tube displacement. Time to decannulation and duration of inpatient stay were similar in both groups. Notably, an analysis of tracheostomy tube displacement identified high body mass index (BMI) and bilateral neck dissection as potential risk factors, and all cases occurred on postoperative day one. To mitigate this risk we recommend implementation of a percutaneous tracheostomy management protocol, precise tube selection using preoperative imaging, and careful passage of the stoma intraoperatively. In conclusion, this study found that the percutaneous technique exhibited a similar complication profile. It remains unclear whether the rates of longer-term complications, such as delayed stoma healing and tracheal stenosis, differ between techniques. A future prospective study with appropriate elimination of selection and reporting bias would help address this and similar pertinent issues, including patients' perspectives.