Total ectopia of thyroid is a rare phenomenon and malignant change in an ectopic thyroid is even rarer. We report a case of medullary carcinoma in a total ectopic lingual thyroid occurring in a 45-year-old woman who presented with dysphagia, plummy voice and a round sessile mass at the base of the tongue. The mass was extirpated using Trotter's midline approach. Upon examination, it was found to be medullary carcinoma in an ectopic thyroid. Permanent substitution therapy with thyroxine secured the euthyroid status of the patient. The embrylogical basis and a review of literature regarding carcinomatous change in an ectopic thyroid are also discussed. There is a need to investigate for an ectopic thyroid, or even total ectopia, in the case of any smooth mass found at the base of the tongue.