Because of the low mortality rate of well-differentiated thyroid cancer (WDTC), investigation of the clinical course leading to death is limited. We analyzed the cause of death and clinical course from diagnosis to death in patients who died of WDTC. A total of 592 WDTC patients died between 1996 and 2018. After exclusion, 79 patients were enrolled and divided into four groups based on their clinical course; that is, inoperable at the time of diagnosis (inoperable), distant metastasis (DM) detected at the time of diagnosis (initial-DM), DM detected during follow-up (late-DM), and loco-regional disease (L-R). Lung (55.6%) in papillary thyroid carcinoma (PTC) and bone (46.7%) in follicular thyroid carcinoma (FTC) were the most common metastasis locations. The most common causes of death were respiratory failure (32.3%) and airway obstruction (30.6%) in PTC, and complications due to immobilization arising from bone metastasis (35.3%) in FTC. Brain metastasis was found in 13.3% of patients and had the worst prognosis. The overall survival (OS) differed significantly (p = 0.001) according to clinical course; the inoperable had the shortest survival, followed by the initial-DM, L-R, and late-DM. However, OS did not differ significantly between PTC and FTC patients with initial-DM (p = 0.83). Other causes of death were far more common than death resulting from WDTC. In patients dying of WDTC, the major cause of death varied by metastatic site. OS differed according to clinical course, but not histologic type. Timing and DM sites differed between PTC and FTC.