Although early complications of microvascular free flaps and regional pedicled flaps of the head and neck are well described in the literature, there is relatively limited knowledge regarding their long-term complications. We describe the case of a 62-year-old gentleman who underwent primary resection and adjuvant radiation therapy for supraglottic squamous cell carcinoma who subsequently underwent salvage total laryngectomy with pectoralis major muscle flap reconstruction. During a later esophageal dilation for complaints of dysphagia, a new exophytic lesion of the hypopharynx was biopsied on endoscopy. The lesion was excised via transoral robotic surgery with final pathology revealing squamous cell carcinoma completely confined to the skin paddle of the pectoralis flap and arising from the epidermis of the skin flap. No further therapy was undertaken and there has been no evidence of recurrence 2 years after resection. Synchronous cutaneous malignancy is a rare complication of free and pedicled flap reconstruction, however its diagnosis is increasing. Given the concern for recurrent mucosal tumors arising in the upper aerodigestive tract which may require extensive resection with or without adjuvant therapy, it is important to determine the etiology of the underlying malignancy to guide appropriate treatment.