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Introduction Limited data are available regarding the prevalence of thrombotic/cardiovascular disease and treatment patterns for patients with coronavirus disease 2019 (COVID-19) in Japan. In this study we describe patients hospitalized for COVID-19 in Japan. Methods This retrospective database study analyzed the Japan Medical Data Vision database (416 acute care hospitals) for patients hospitalized for COVID-19 during the identification period from 1 January 1 to 30 September 2020. Results Among 9282 eligible patients, 832 (9%) had developed thrombotic disease including myocardial infarction, ischemic stroke, deep vein thromboembolism and pulmonary embolism. Intriguingly, 171(1.8%) had two thrombotic events and 25 (0.3%) had three or four thrombotic events at the same time. The data also showed that arterial thrombotic events accounted for 77% of total thrombotic events. Anticoagulant and/or antiplatelet medication was provided to 3312 patients. Even with antithrombotic medication, 21.2% of patients suffered from thrombotic diseases. Conclusions Patients with COVID-19 could experience thrombotic complications in every blood vessel. Further optimization of medication is crucial for preventing thrombotic complications and improving prognosis.