Abstract Background Autoimmune disease, including autoimmune thyroid disease, with uncharacteristic symptoms can be due to additional severe disease. We report a life-threatening debut of autoimmune polyglandular syndrome type II (APS II) defined as Addison’s disease combined with autoimmune diabetes and/or thyroid disease. Patient findings A 33-year-old male with newly diagnosed hypothyroidism was referred to a tertiary center due to fatigue and 20-kg rapid weight loss. Malignancy was excluded. After a gastroscopy, he developed Addison’s crisis; he was admitted to our hospital and stabilized. Final diagnoses included Hashimoto’s thyroiditis, Addison’s disease, vitiligo, and pernicious anemia. Whole genome sequencing found no genetic variants associated with component diseases. Human leukocyte antigen typing revealed DR3/DR4 and DQ8/DQ2 heterozygosity associated with APS II. Summary A patient with Hashimoto’s thyroiditis and weight loss presented with Addison’s crisis and was diagnosed with APS II. Conclusions Awareness of potential polyautoimmunity in clinical evaluation of patients with thyroid disease improves diagnosis and can be lifesaving.