Second primary squamous cell carcinoma (SCC) in the skin of a flap used for reconstruction of floor of mouth is rare. A case of SCC arising in the pectoralis major myocutaneous flap that was used to reconstruct the floor of mouth 12 years after subtotal glossectomy and resection of the floor of mouth is reported. The tumour is a second primary SCC arises in the skin of a myocutaneous flap without any obvious risk factors. Review of the literature reveals four previous similar reports and the findings are summarized. In summary, squamous epithelium of the skin flap after prolonged exposure to non-physiological stimuli may lead to metaplasia and possible carcinoma formation. Long-term follow up and awareness of this complication are needed for head and neck cancer patients after resection and reconstruction.