Thyroid storm (TS) is an endocrine emergency requiring aggressive medical management. In severe cases, hemodynamic instability may necessitate extracorporeal membrane oxygenation (ECMO) support as a bridge to definitive surgical treatment. ECMO is categorized into two types: venoarterial (V-A) ECMO, which provides both cardiac and pulmonary support, and venovenous (V-V) ECMO, which supports only pulmonary function. Surgery is generally not recommended for patients with unstable TS due to the high risk of complications, even when ECMO support is in place. Here, we present a case of a 44-year-old man initially improved with V-A ECMO for TS with cardiogenic shock, but later developed refractory hypoxemia due to pulmonary thromboembolism (PTE). He subsequently underwent emergency thyroidectomy with continuous support from V-V ECMO.