We estimated age-adjusted mortality and investigated the dominant causes of death as well as comorbidities among people with epilepsy (PWE) in Lithuania, a country with frequent deaths from external causes. From 2016 to 2019, the age-adjusted rate of death among PWE in Lithuania was compared with mortality data in the general population. Each year of analysis, individuals who were diagnosed with epilepsy comprised a retrospective cohort. The standardized mortality ratio (SMR) of PWE varied from 2.93 (95% CI 2.78 to 3.07) to 3.18 (95% CI 3.02 to 3.34). PWE died at least one decade earlier than expected in the general population. The dominant causes of death were cardiovascular diseases (their proportion ranged from 44.8% to 49.3%), cancer (16.7% to 21.3%) and external causes of death (8.5% to 10.9%). The proportion of the latter decreased over time (r = −0.99, p = 0.01), whereas the SMR for external causes of death remained relatively constant. Epilepsy was the underlying cause of death in 163 cases (2.6%), and noted as a condition contributing to death in 1010 cases (15.9%). Cerebrovascular and cardiological conditions and dementia were the most frequent comorbidities among PWE before their death. Epilepsy-unrelated causes of death are relevant contributors to mortality among PWE. There is a need for PWE-oriented societal interventions to reduce the frequency of external deaths beyond the trend in the general population.