The 2013-2016 Ebola Virus Disease (EVD) epidemic in West Africa was the deadliest in history, with over 28,000 cases. Numerous physical and mental health symptoms have been reported in EVD survivors, although there is limited prior research on how the health of survivors compares to the general population. We conducted a survey of EVD survivors in Kenema District, Sierra Leone and a population-based sample of community members who lived in EVD-affected areas but were not diagnosed with EVD, and compared resulting data about self-reported symptoms, duration, and severity between EVD survivors and community members through multivariate regression models. This study found that more than six years after the epidemic, survivors were significantly more likely to experience both physical and mental health symptoms than community members, with respective adjusted incidence rate ratios (IRRs) of 2.65 (95% CI, 2.28-3.09), p < 0.001, and 11.95 (95% CI, 6.58-21.71), p < 0.001. The most highly reported physical health symptoms experienced by EVD survivors were joint pain (75.5%), headaches (67.3%), and vision problems (44.5%), and the most prevalent psychological symptoms were spells of terror and panic (25.5%) and difficulty falling asleep or staying asleep (20.0%). EVD survivors were significantly more likely than community members to report the symptoms as lasting for a longer period, a median of 6.0 (3.0-7.0) years, and with higher severity. The results indicated that six years after the epidemic, EVD survivors in Kenema District, Sierra Leone are experiencing worse physical and mental health than their peers. These findings of the long-term, debilitating health issues following EVD infection should be considered when designing and implementing future epidemic responses.