Prolonged fever in patients can be a diagnostic challenge. Clinicians generally consider infectious diseases, malignant diseases and collagen vascular diseases as possible causes of pyrexia of unknown origin (PUO). Even after extensive evaluation as many as 15 percent of patients with prolonged fever may remain undiagnosed. This case report describes subacute thyroiditis as a cause of prolonged fever and documents how that diagnosis was finally made after 40 days of fever.