Squamous cell carcinoma represents the most common cancer affecting the oral cavity. At the University of Naples “Federico II”, two different antibiotic protocols were used in patients undergoing oral mucosa cancer surgery from 2006 to 2018. From 2011, there was a shift; the combination of Cefazolin plus Clindamycin as a postoperative prophylactic protocol was chosen. In this paper, a health technology assessment (HTA) is performed by using the Six Sigma and DMAIC (Define, Measure, Analyse, Improve, Control) cycle in order to compare the performance of the antibiotic protocols according to the length of hospital stay (LOS). The data (13 variables) of two groups were collected and analysed; overall, 136 patients were involved. The American Society of Anaesthesiologist score, use of lymphadenectomy or tracheotomy and the presence of infections influenced LOS significantly (p-value < 0.05) in both groups. Then, the groups were compared: the overall difference between LOS of the groups was not statistically significant, but some insights were provided by comparing the LOS of the groups according to each variable. In conclusion, in light of the insights provided by this study regarding the comparison of two antibiotic protocols, the utilization of DMAIC cycle and Six Sigma tools to perform HTA studies could be considered in future research.