Women veterans report high rates of persistent pain and high rates of sexual trauma. We sought to determine whether the presence and intensity of persistent pain, as well as level of pain-related interference, in the VA Connecticut Women's Clinic population was positively associated with reports of sexual trauma. Women presenting for routine appointments at the VA Connecticut Women's Health Center were recruited for study. Participants (N = 213) provided detailed information about their demographic, psychosocial, clinical, pain, and sexual trauma status. Bivariate and multivariate analyses were conducted to determine whether a report of sexual trauma was independently associated with the presence of pain, and levels of pain intensity and pain-related interference. A substantial majority (78%) reported an ongoing pain problem, whereas the prevalence of any reported sexual trauma was 36%. In bivariate analysis, persistent pain was associated with a greater number of chronic conditions (P < 0.01), depression symptom severity (P < 0.05), a history of military sexual harassment (P < 0.05), and military forced sex (P < 0.05). In a multivariate logistic regression analysis, persistent pain was independently associated with having at least two (OR 3.32, 95% CI 1.11, 9.90), or three or more chronic conditions (OR 7.56, 95% CI 2.34, 24.4) and depressive symptom severity score (OR 1.10, 95% CI 1.02, 1.19), but was not associated with sexual trauma (OR 1.70, 95% CI 0.66, 4.42). In multivariate linear regression analyses that included only those who reported pain at the time of the assessment, white race (P < 0.05) and sexual trauma histories (P < 0.05) were significantly associated with level of pain intensity, whereas being married (P < 0.01) was negatively associated with pain intensity. Depressive symptom score (P < 0.001) and sexual trauma (P < 0.05) were also significantly associated with level of pain interference. Reported sexual trauma is prevalent and while not independently associated with the presence of pain among women veterans in our study, for those who have pain, it is associated with greater pain intensity and pain-related interference.