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Introduction Tobacco smoking poses a significant risk for various diseases, including cardiovascular diseases, chronic respiratory diseases, and cancers. In Kenya, tobacco-related deaths contribute substantially to non-communicable disease mortality. This study aims to quantify the mortality attributed to tobacco smoking in Kenya from 2012 to 2021. Methods Employing a prevalence-based analysis model, the study utilized population attributable fraction (PAF) to estimate age-specific smoke attributable mortality (SAM) rates for individuals aged ≥35 years. Causes of death associated with tobacco use, including cancers, cardiovascular diseases, respiratory diseases, tuberculosis, and diabetes, were analyzed based on age, sex, and death records between 2012 and 2021. Results Over the study period, 60228 deaths were attributed to tobacco-related diseases, with an annual increase observed until 2016 and subsequent fluctuations. Respiratory diseases, diabetes mellitus, malignant cancers, tuberculosis, and cardiovascular diseases collectively accounted for 16.5% of deaths among individuals aged ≥35 years. Notable contributors were pneumonia and influenza (respiratory diseases), esophageal cancer (cancers), and cerebrovascular diseases (cardiovascular diseases). Of the observed deaths, 16.5% were attributed to smoking, with respiratory diseases (40.5%), malignant cancers (31.4%), tuberculosis (13%), cardiovascular diseases (8.9%), and diabetes mellitus (6.1%) contributing. Pneumonia and influenza, esophageal cancer, chronic airway obstruction, and tuberculosis were primary causes, comprising 70% of all SAM. Conclusions Tobacco-related mortality is a significant public health concern in Kenya. Efforts should focus on preventing tobacco use and managing associated disease burdens. Smoking cessation initiatives and comprehensive tobacco control measures are imperative to mitigate the impact on population health.