The epidemiology of drug-induced anaphylaxis using the Japanese nationwide database has been not reported, even though drugs are a common trigger of anaphylaxis. The aim of this study was to describe the epidemiological profile of cases of drug-induced anaphylaxis, including fatal cases, using the data from the Japanese Adverse Drug Event Report database (JADER). We extracted data regarding drug-related adverse events, between April 2004 and February 2018, published in JADER by the Pharmaceuticals and Medical Devices Agency. We analyzed cases of anaphylaxis occurring between January 2005 and December 2017. The drug classification was based on the Japanese Standard Commodity Classification. There were 16,916 cases of anaphylaxis reported during the study period. Among them, 418 fatalities were registered. The incidence of drug-induced anaphylaxis and fatal cases was 1.03 cases/year per 100,000 population and 0.03 cases/year, respectively. The most frequent causes of anaphylaxis were diagnostic agents, including X-ray contrast media (20.3%), and biological preparations, such as human blood preparations (20.1%). In fatal cases, diagnostic agents (28.7%) and antibiotic preparations (23.9%) were the most commonly associated types of drugs. The frequency of drug-induced anaphylaxis and fatalities in Japan remained unchanged over the 13-year period analyzed in this study. Diagnostic agents and biological preparations were the most frequent causes of anaphylaxis; however, fatalities were most frequently caused by either diagnostic agents or antibiotic preparations.