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Background The purpose of this study was to compare postoperative morbidities and functional outcomes of pectoralis major myocutaneous (PMMC) flap and cutaneous free flap reconstruction approaches in hypopharyngeal squamous cell carcinoma patients. Methods We retrospectively reviewed records from 99 patients who underwent hypopharyngeal reconstruction with a cutaneous free flap (n=85) or PMMC flap (n=14) between 1995 and 2013. Morbidity was classified into hospitalization, medical, or flap-related complications. Functional outcomes were classified into oral re-alimentation and decannulation time. Results The overall flap-related complication rate was higher in the PMMC flap group (n=8, 57.1%; P=0.019), but the medical morbidity rate was higher in the cutaneous free flap group (n=68, 80%; P=0.006). The rate of pneumonia was higher in the cutaneous free flap group (n=48, 56.5%; P=0.020). Pulmonary premorbidity was the variable most significantly associated with pneumonia (odds ratio=3.012, P=0.012). There was no statistically significant difference in oral re-alimentation and decannulation time between the two groups. Conclusions Although the functional superiority of free flaps has been reported in many studies, our results do not support this hypothesis. One limitation of our study is the relatively smaller flap size and fewer PMMC flap cases compared with the cutaneous free flap group. The low postoperative medical morbidity incidence rate in the PMMC flap group was clinically significant; however, the free flap group had more flap-related complications. Thus, PMMC flaps should be considered a viable option, especially for patients with pulmonary premorbidities.