Background: Collision medullary and papillary thyroid carcinoma (MTC/PTC) is a rare entity, constituting less than 1% of all thyroid malignancies. The concurrent presence of these malignancies in patients with autoimmune thyroid disease, such as Graves’ disease, is even more uncommon. Calcitonin (Ctn) is considered one of the key MTC biomarkers. Mixed tumors may alter this relationship. Case Description: We report the case of a 55-year-old female with a history of Graves’ disease, who underwent total thyroidectomy for persistent dysthyroid orbitopathy. Histopathological analysis revealed a 9-mm collision MTC/PTC tumor in the left thyroid lobe, confirmed through immunohistochemical staining. Postoperative evaluation demonstrated lymph node metastases, necessitating central and left lateral neck dissection. Postoperative serum markers (calcitonin, carcinoembryonic antigen, thyroglobulin) declined significantly following surgery and radioiodine therapy. Conclusion: Subcentimeter collision MTC–PTC tumors can be aggressive, challenging size-based management thresholds. Treatment should integrate MTC and PTC protocols, with Ctn, carcinoembryonic antigen (CEA), and thyroglobulin monitored in tandem. Larger datasets are needed to refine Ctn prognostic thresholds in mixed tumors.