Thyroid storm is a life-threatening and emergent manifestation of thyrotoxicosis. However, predictive features associated with fatal outcomes in this crisis have not been clearly defined because of its rarity. The objective of this study was to investigate the associations of patient characteristics, treatments, and comorbidities with in-hospital mortality. We conducted a retrospective observational study of patients diagnosed with thyroid storm using a national inpatient database in Japan from April 1, 2011 to March 31, 2014. Of approximately 21 million inpatients in the database, we identified 1324 patients diagnosed with thyroid storm. The mean (standard deviation) age was 47 (18) years, and 943 (71.3%) patients were female. The overall in-hospital mortality was 10.1%. The number of patients was highest in the summer season. The most common comorbidity at admission was cardiovascular diseases (46.6%). Multivariable logistic regression analyses showed that higher mortality was significantly associated with older age (≥60 years), central nervous system dysfunction at admission, nonuse of antithyroid drugs and β-blockade, and requirement for mechanical ventilation and therapeutic plasma exchange combined with hemodialysis. The present study identified clinical features associated with mortality of thyroid storm using large-scale data. Physicians should pay special attention to older patients with thyrotoxicosis and coexisting central nervous system dysfunction. Future prospective studies are needed to clarify treatment options that could improve the survival outcomes of thyroid storm.