A 22-year-old patient underwent fine needle aspiration of a nodule at the outer center of the right lobe of the thyroid, and it was reported to be Bethesda system category IV, Hurthle cell follicular neoplasia. The patient, who persented to Onsekiz Mart University Research and Application Hospital, underwent surgery. During right total thyroidectomy, an almost totally infarcted nodule and papillary structures around these infarcted areas were detected. Herein, we report on diagnostic challenges faced in confirming whether the infarcted nodule was a case of reactive papillary changes or an underdiagnosed papillary carcinoma and how the challenges were overcome using immunohistochemistry analysis and molecular genetic testing. In addition, we examined the case along with a literature review because an accompanying synchronous brain stem astrocytoma was detected in the patient after thyroidectomy.