Background Ebola Virus Disease (EVD) is a deadly and feared infectious disease, which can be responsible of debilitating physical and psychological sequelae in survivors including depression and anxiety disorders. Unfortunately, there are scarce data on survivor sequelae in Democratic Republic of the Congo. So this study assessed PTSD, depression and anxiety symptoms among EVD survivors enrolled in the follow-up program of the psychosocial care team of Beni town’s general hospital. Methods A cross-sectional study used consecutive sampling to recruit 144 Ebola virus disease survivors from October 23 to November 13; 2019. Basic socio-demographic data, presence of headache and short-term memory function were assessed. The Post-traumatic Checklist Scale and Hospital Anxiety and Depression Scale were used to assess psychological burden among participants. Descriptive statistics and a binary logistic regression model were used for analysis. Results The prevalence of PTSD, depression and anxiety was 24.3%, 24.3% and 33.3% respectively. Being male (p = 0.049 ; OR = 0. 42 (CI : 0. 16–0.95), suffering from persistent headache (p = 0. 014 OR = 2.62 CI (1.12–6.14), losing a loved one because of EVD (p = 0. 015 ; OR : 2.60 (CI : 1.11–6.15) and being young − 18–24 years - (p = 0,026 ; OR : 0. 261 (IC : 0. 018-0.055).) were statistically associated with PTSD diagnosis. Having short-term memory impairment and suffering from persistent headache were statistically associated with depression and anxiety diagnoses (p = 0.026 OR = 2,44 (CI : 1.03–5.82) ; (p = 0. 025 OR = 2.24 (CI : 1.04–4.85) ; (p = 0.014 OR = 2.62 (CI : 1.12–6.14) ; (p = 0. 020 OR = 2.31 (CI : 1.06–5.01) Conclusion The prevalence of PTSD, depression and anxiety is high among EVD survivors. Development of specialized psychiatric services to sustain psychiatric and psychological health amongst survivors in the cultural context of the Eastern part of the DRC should be considered by the teams fighting against EVD in the DRC.