Background: Alcohol consumption is widely recognized as a leading cause of premature mortality and a significant global health concern. This study aimed to investigate the trends in alcohol use disorders, including incidence, mortality, and disability-adjusted life years (DALYs), in Estonia from 1990 to 2019 using data from the Global Burden of Disease (GBD) dataset. Methods: The GBD study is a comprehensive epidemiological research effort that analyzes various causes of death, diseases, injuries, and risk factors across multiple countries and territories. In this study, we utilized the GBD dataset to estimate annual incidence, prevalence, mortality, years of life lost, years living with disabilities, and DALY rates by gender and age from 1990 to 2019. To assess the trends in these indices, including DALY, incidence, mortality, and 1-mortality-to-incidence ratio (1-MIR), joinpoint regression analysis was employed. This allowed for the identification of significant changes in trends at specific time points and the calculation of annual percent change between these points. Results: Our findings revealed an overall decreasing trend in the incidence rate of alcohol use disorder over the study period. However, the average DALY, mortality, and 1-MIR trends did not exhibit significant variation during this time. Moreover, we observed a more substantial decline in alcohol use disorders among men compared to women from 1990 to 2019. Specifically, the incidence of alcohol use disorders demonstrated a significant increase from 1990 to 2000, followed by a decline from 2010 to 2018, and continued to decrease from 2017 to 2019. Conclusion: This study provides important insights into the changing trends of alcohol use disorders, including incidence and mortality, in Estonia from 1990 to 2019. Our findings indicate a decreasing pattern over time, suggesting a positive shift in alcohol consumption behavior. Additionally, we observed that men had higher rates of MIR, DALY, mortality, and incidence of alcohol use disorders compared to women. These results emphasize the need for targeted health prevention programs to sustain and further promote the downward trend in alcohol-related disorders.