Introduction: The mortality rates associated with cardiovascular disease (CVD) and diabetes exhibit disparities by region, with Central Africa ranking fourth globally in terms of mortality rate. The Democratic Republic of Congo (DRC) does not possess mortality data pertaining to these specific underlying causes of death. This study aimed to determine the death rate attributable to CVD and diabetes in two cities in the DRC. Methodology: The data on CVD and diabetes utilized in this study were obtained from a pilot project and were registered in the National Health Information System (NHIS). Data quality was initially evaluated using an automated Digital Open Rule Integrated Selection (DORIS), followed by an assessment conducted manually by three assessors. Descriptive and comparative analyses were carried out to determine the proportion of mortality related to CVD and diabetes. Results: CVD accounted for 20.4% (95%CI: 17.7–23.4%) of deaths in the two cities (Kinshasa and Matadi), whereas diabetes accounted for 5.4% (95%CI: 3.9–7.2%). After adjusting for age and city, the proportional mortality from CVD and diabetes was higher for women than men and increased with age. This study recorded 4.4% of deaths among men and 7.0% among women as the proportional mortality from diabetes. Conclusions: Non-communicable diseases (NCDs) continue to be a major cause of death, and CVD and diabetes are among the leading causes of early mortality in adults in urban areas. The proportional mortality related to CVD and diabetes appears to be higher in women than in men. Special emphasis should be placed on women, particularly during adulthood, to ensure the prompt detection of diabetes and cardiovascular conditions.