Introduction: Autoimmune thyroid diseases (AITD) are the most common causes of thyroid gland dysfunctions and non-endemic goiter, which result from dysregulation of the immune system leading to an immune attack on the thyroid. We present a case of an unusual presentation of AITD of a patient presented with pyrexia of unknown origin. Case Presentation: A 40-year previously well female presented to the Professorial Medical Unit Peradeniya with six weeks of bilateral lower limb pain with eight weeks of fever which subsided two weeks before the presentation, associated with lethargy, tiredness, and intermittent episodes of sweating. On examination, her blood pressure was 120/80 mmHg, pulse rate was 80 bpm, and she had tenderness over bilateral thighs and calves. The diagnostic workup revealed low TSH 0.004 µIU/L, T4 20.93 µIU/L, ESR 90 mm/h, CRP 45.1 mmol/L, and anti-thyroid peroxidase antibody (Anti-TPO) level was positive with 32 IU/ml. Therefore, the patient was treated as hyperthyroidism with autoimmune thyroid disease, and she improved with one week of treatment with carbimazole and prednisolone. After two weeks, a free T3 level was done on the review, which revealed a low value indicating Hashitoxicosis as the possible diagnosis. Conclusion: Anti-TPO antibodies can be positive in Hashimoto’s thyroiditis, and Graves’ disease and differentiation can be done using other clinical parameters and preferably by radionuclide studies. Autoimmune thyroid diseases could be presented with unusual manifestations where fever and myalgia would be the only presentation. Therefore, it is essential to have a prompt clinical suspicion and perform serum investigations to exclude any thyroid disease.