Afghanistan faces a critical health challenge due to different diseases, including diseases caused by infectious diseases, worsened by the structural limitations typical pattern in low- and middle-income countries. This secondary analysis of modeled 2023 estimated assessed data to evaluate changes in Disability-Adjusted Life Years (DALYs), Years Lived With Disability (YLDs), and Years of Life Lost (YLLs) in Afghanistan in 1999 and 2023. We used multiple regression using SPSS Software Version 28 (IBM Corp., Armonk, NY), and the results revealed that the Afghan population has experienced a statistically significant improvement in health outcomes for diseases caused by infectious diseases, with reductions in DALYs (64.8%), YLDs (47.9%), and YLLs (65.0%). The results were consistent with those of neighboring countries, suggesting the effectiveness of access to health sector services. The decrease in the burden of infectious diseases in Afghanistan can be attributed to improved access to curative medicine services and proactive public health measures, such as vaccination programs, access to clean sanitation systems, and better health literacy. The result did not show statistically significant gender differences in YLLs, YLDs, or DALYs, which challenges the conventional understanding of gender-based health disparities in access to care. The sustainability of Afghanistan's health gains can be threatened if persistent political instability and critical gaps in medical infrastructure continue.