ABSTRACT: Background and Objectives: Reduction in health inequalities is a highly important task in public health policies worldwide. In Lithuania, inequalities in mortality by place of residence are among the greatest, compared to other European Union (EU) countries. However, studies on inequalities in mortality by place of residence over a long-term period have not been investigated in Lithuania. The aim of this study was to present changes in mortality inequalities in urban and rural populations during 1990-2018. Materials and Methods: Mortality rates from all causes, cardiovascular diseases, cancer, external causes, and gastrointestinal diseases in urban and rural population by sex were calculated per 100,000 populations and were standardized by age. Inequalities in mortality were assessed using rate differences and rate ratio. For the assessment of inequality trends during 1990-2018, the joinpoint regression analysis was applied. Results: Mortality between urban and rural populations varied. In rural areas, mortality lower than that in urban areas was observed only in 1990 among women, in case of mortality from cancer and gastrointestinal diseases (compared with in 2018) (p < 0.05). In 2018, mortality from all causes, cardiovascular diseases, and external causes in urban and rural areas was lower than in 1990 in both sexes. However, mortality from gastrointestinal diseases was higher (p < 0.05). In 2018, mortality from cancer among both sexes was lower only in urban areas (p < 0.05). Mortality inequalities between rural and urban areas decreased statistically significantly only among men from external causes and from all causes (respectively, on average, by 0.52% per year and, on average, by 0.21% per year). Meanwhile, mortality from cardiovascular and gastrointestinal diseases increased in both sexes, and mortality from cancer and all causes of death increased among women. The increase in the inequalities of mortality from gastrointestinal diseases was the most rapid: among men-on average, by 0.69% per year, and among women-on average, by 1.43% per year, p < 0.0001. Conclusions: During 1990-2018, the inequalities in mortality by place of residence in Lithuania statistically significantly decreased only among men, in terms of mortality from external causes and from all causes. Therefore, reduction in inequalities in mortality must be the main the health policy challenge in Lithuania.