Background In conflict-affected settings, women and girls are vulnerable to gender-based violence (GBV). GBV is associated with poor long-term mental health such as anxiety, depression and post-traumatic stress disorder (PTSD). Understanding the interaction between current violence and past conflict-related violence with ongoing mental health is essential for improving mental health service provision in refugee camps. Methods Using data collected from 209 women attending GBV case management centres in the Dadaab refugee camps, Kenya, we grouped women by recent experience of GBV using latent class analysis and modelled the relationship between the groups and symptomatic scores for anxiety, depression and PTSD using linear regression. Results Women with past-year experience of intimate partner violence alone may have a higher risk of depression than women with past-year experience of non-partner violence alone (Coef. 1.68, 95% CI 0.25 to 3.11). Conflict-related violence was an important risk factor for poor mental health among women who accessed GBV services, despite time since occurrence (average time in camp was 11.5 years) and even for those with a past-year experience of GBV (Anxiety: 3.48, 1.85–5.10; Depression: 2.26, 0.51–4.02; PTSD: 6.83, 4.21–9.44). Conclusion Refugee women who experienced past-year intimate partner violence or conflict-related violence may be at increased risk of depression, anxiety or PTSD. Service providers should be aware that compared to the general refugee population, women who have experienced violence may require additional psychological support and recognise the enduring impact of violence that occurred before, during and after periods of conflict and tailor outreach and treatment services accordingly.