The incidence of primary papillary carcinoma arising in thyroglossal cyst is rare and occurs in <1% of thyroglossal cysts. Even rarer is its diagnosis by pre-operative fine needle aspiration cytology (FNAC). Only 15 such cases diagnosed by FNAC have been previously reported in the literature. In this article, cytomorphology of the current case is presented along with a review of the literature on FNAC and its diagnostic pitfalls.