Background There is limited data available on the long-term mental health impact of Ebola virus disease (EVD) on survivors despite the disease experience of survivors meeting the criteria of a traumatic event as defined in the Diagnostic and Statistical Manual of Mental Disorders version IV (DSM IV). This study aimed to assess the prevalence and predictive factors of anxiety, depression and posttraumatic stress disorder among EVD survivors, approximately 2 years after discharge from the Ebola treatment centre (ETC). Methods We conducted a cross-sectional study between May and August 2017 among 197 adults Ebola survivors in Bombali district, Northern Sierra Leone. We collected information about demographics, mental health status and possible predictive factors. The HAD scale was used to measure anxiety and depression. PTSD was measured using the PTSD-checklist (PCL). Chi-square test or Fisher exact two-tailed tests were used to test for associations and the multiple logistic regressions model to determine factors that were independently associated with the outcome variables. Results The mean anxiety, depression and PTSD scores were (5.0 ± 3.9), (7.1 ± 3.8) and (39.5 ± 6.4) respectively. Based on cut-off scores, the prevalence of anxiety (HADs score ≥ 8), depression (HADs score ≥ 8) and PTSD (PCL ≥ 45) among Ebola survivors were (n = 49, 24.9%), (n = 93, 47.2%) and (n = 43, 21.8%) respectively. Older Ebola survivors (≥30 years) were more likely to show symptoms of depression (AOR = 8.5, 95% CI: 2.68–27.01, p = 0.001) and anxiety (AOR = 3.04; 95%CI: 1.2–7.7, p = 0.019) compared to younger ones (< 30 years). In addition, Ebola survivors who experienced a decreased level of exercise post-ETC discharge were more likely to show symptoms of depression (AOR = 2.63; 95%CI: 1.25–5.54, p = 0.011) and anxiety (AOR = 3.60; 95%CI: 1.33–9.72, p = 0.012) compared to those whose exercise remained the same post-ETC discharge. Conclusion Our findings show that anxiety, depression and PTSD are common among the Ebola survivors in Bombali district, Northern Sierra Leone, and that underscores the need to diagnose and manage mental health morbidities among Ebola survivors long after their recovery from Ebola virus disease. Cognitive Behaviour Therapy (CBT) and Interpersonal Therapy (IPT) need to be explored as part of overall mental healthcare package interventions.