Objective: This study used a long-term trend analysis to investigate whether gender differences were related to the risk of injury and epidemiological characteristics in Taiwan from 1998 to 2015. Materials and methods: Data on 4,647,259 hospitalized patients that were injured from 1 January 1998, to 31 December 2015 were collected from the National Health Insurance Research Database (NHIRD). Among the injured patients, 2,721,612 males and 1,925,446 females were identified. Patients were age-, gender-, and index date-matched. Multiple logistic regression was used to analyze the risks of injury via gender differences. A p-value < 0.05 was considered significant. Results: The injury risk of the male patients was 1.4 times higher than that of female patients (AOR = 1.427, 95% CI = 1.40–1.44). The rising trend of male injured hospitalized patients was also greater than that of female injured hospitalized patients. Conclusion: Males were more at risk of injury than females. Gender differences were related to the increased risk of epidemiological characteristics of injury.