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Background The 2013–2016 Ebola virus disease (EVD) epidemic resulted in more infections and deaths than all prior outbreaks in the 40-year history of this virus combined. This study examines how experiences of EVD infection, and preventive measures such as social distancing, were linked to experiences of stigma and social exclusion among those reintegrating into their communities. Methods Key informant interviews (n = 42) and focus group discussions (n = 27) were conducted in districts with a high prevalence of EVD and representing geographical and ethnic diversity (n = 228 participants). The final sample was composed of adults (52%) and children (48%) who were EVD-infected (46%) and -affected (42%) individuals, and community leaders (12%). Data were coded using a Grounded Theory approach informed by Thematic Content Analysis, and analyzed using NVivo. Interrater reliability was high, with Cohen’s κ = 0.80 or higher. Findings Participants described two main sources of EVD-related stress: isolation from the community because of social distancing and other prevention measures such as quarantine, and stigma related to infected or affected status. Participants linked experiences of social isolation and stigma to significant distress and feelings of ostracization. These experiences were particularly pronounced among children. Sources of support included community reintegration over time, and formal community efforts to provide education and establish protection bylaws. Interpretation This study found that social distancing and EVD-related stigma were each prominent sources of distress among participants. These results suggest that isolation because of infection, and the enduring stigmatization of infected individuals and their families, demand coordinated responses to prevent and mitigate additional psychosocial harm. Such responses should include close engagement with community leaders to combat misinformation and promote community reintegration.