Inverted papilloma is a rare and benign tumour. It affects the nasal cavity and paranasal sinuses, has a high rate of recurrence and is associated with malignant transformation. Only few cases of a poorly differentiated carcinoma arising from inverted papilloma have been reported, none of which in the nasopharynx. We report a case of a 37-year-old female, who presented originally in 2012 with inverted papilloma of the nasal septum which was surgically resected. Nasopharyngeal biopsy from 2014 was reported as carcinoma in situ and treated with local endoscopic resection. Three years later she presented with a solitary lesion of the right Eustachian tube opening, confirmed as invasive poorly differentiated carcinoma. Imaging revealed T4 N2b M0 malignancy with skull base and prevertebral space invasion, likely extension into right temporal lobe and malignant adenopathy. Although rare, malignant transformation of inverted papilloma in unusual places should be considered during workup and monitoring of patients.