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Autoimmune polyglandular syndrome type 2 (APS 2) is a rare endocrinopathy characterized by primary adrenal insufficiency associated with autoimmune thyroiditis or type 1 diabetes. The diagnosis is usually delayed, and it has high mortality if undetected. Hashimoto's thyroiditis is the commonest thyroid disease associated with APS 2, while structural thyroid abnormalities or neoplasms are rarely reported. Hurthle cell adenoma (HCA) is a rare benign oncocytic tumor and may arise from long-standing chronic autoimmune thyroiditis. To date, there is no documented case of APS 2 with Hurthle cell adenoma, making this case a rarity. We present a case of a 44-year-old man with gastrointestinal symptoms, fatigue, hyperpigmentation, and weight loss for six months. The critical findings were generalized hyperpigmentation with orthostatic hypotension and electrolyte imbalance, especially hyponatremia and hyperkalemia, with low cortisol and elevated adrenocorticotropic hormone levels. These, along with bilateral adrenal atrophy on imaging and high anti-thyroid peroxidase antibodies, established a diagnosis of primary adrenal insufficiency and autoimmune thyroiditis, findings consistent with APS 2. HCA was detected on fine needle biopsy subsequently, which is a rare association in APS 2. The patient responded well to adrenal and thyroxine replacement therapy. The patient's tumor, although small and asymptomatic, was excised via hemithyroidectomy as per the American Thyroid Association guidelines. Histopathology confirmed HCA with no capsular invasion. Postoperative recovery was uneventful, and on follow-up, the patient showed significant improvement. There are two major learning points from this case. Firstly, it emphasizes the need for high clinical suspicion in diagnosing APS 2 in patients with nonspecific constitutional symptoms. Secondly, it highlights the rare but clinically significant co-occurrence of HCA with APS 2. HCA, while benign, can mimic malignancy on cytology and requires histopathological confirmation. In view of the possibility of progression of HCA to Hurthle cell carcinoma, surgical excision is the standard of care.