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We describe the first documented case of sinking skin flap syndrome (SSFS) following head and neck cancer resection with free flap reconstruction. This rare syndrome, also known as “syndrome of the trephined,” is an uncommon complication typically seen after decompressive craniectomy prior to cranioplasty. Thought to be related to atmospheric pressure and gravity overwhelming intracranial pressure, the scalp is displaced inward, and cortical compression can occur over the surgical site, leading to neurologic changes (e.g. headache, mental status changes, seizures, focal deficits) as well as dysautonomia. A 58-year-old male underwent wide local excision of a large, advanced squamous cell carcinoma of the scalp that required craniectomy and dural resection, followed by reconstruction with a latissimus dorsi myofascial free flap and overlying meshed skin graft. On post-operative day 11, he developed acute right hemiparesis with right facial droop, altered mental status, hypotension and bradycardia, with subsequent CT of the head supporting a diagnosis of sinking skin flap syndrome. He improved within 48 hours with conservative treatment, without long term sequelae. While this is a rare phenomenon, it is important to keep sinking skin flap syndrome in the differential diagnosis for patients who develop neurologic changes or autonomic dysfunction following calvarial resection with soft tissue free flap reconstruction.