BACKGROUND Mucosa-associated lymphoid tissue (MALT) lymphoma is a low-grade B-cell non-Hodgkin’s lymphoma. Autoimmune (Hashimoto’s) thyroiditis is associated with thyroid MALT lymphoma, but co-existence with papillary thyroid carcinoma (PTC) has been less commonly reported. In this case report, we describe a 58-year-old man who presented with a 6-month history of hoarseness and an enlarged thyroid, and was diagnosed with Hashimoto’s thyroiditis, MALT lymphoma, and PTC. CASE REPORT Upon referral to our hospital, he presented with an enlarged goiter and hoarseness. Based on preoperative findings, he was diagnosed with Hashimoto’s thyroiditis, PTC in the left lobe, and possible malignant lymphoma in both thyroid lobes. However, whether the lymph node swelling around the neck and ¹⁸F-fluorodeoxyglucose uptake on positron emission tomography near the pancreas were related to the PTC, malignant lymphoma, or both remained unclear. Total thyroidectomy and lymph node dissection were performed to treat the PTC and to aid in the diagnosis of malignant lymphoma; the patient was diagnosed with PTC and MALT lymphoma, and lymphadenopathy was attributed to MALT lymphoma. The patient underwent postoperative chemotherapy with rituximab alone, and remission was maintained nearly 3 years after surgery. CONCLUSIONS This report highlights the association between Hashimoto’s thyroiditis and thyroid MALT lymphoma, presents a rare finding of coexistent PTC and lymphadenopathy of initially unknown origin, and underscores the importance of histopathology in the diagnosis of these conditions.