Conflict in Iraq has led to a large number of internally displaced Iraqis, with a great impact on their mental health. A few previous studies investigated the gender differences of mental disorders in Iraqi internally displaced persons (IDPs). The aim of this study was to assess gender differences among Iraqi IDPs after the 2014 terrorist attacks in terms of types of traumatic experiences, prevalence of post-traumatic stress disorder (PTSD), and other symptoms of common mental disorders (depression, anxiety, and somatization symptoms). A cross-sectional survey was conducted in April–June 2015 among 358 female and 464 male adult IDPs living in IDP camps in Duhok, Iraq. The Harvard Trauma Questionnaire (HTQ), General Health Questionnaire (GHQ-28), and Self-Reporting Questionnaire (SRQ-20) were applied by local interviewers. Comparison of scores of these measures between the two genders was performed using independent sample t-tests. Logistic regression analysis was carried out to identify predictors for PTSD. Although the types of traumatic events experienced by female and male IDPs were nearly similar, males reported higher exposure to combat situation, torture, oppressions, and destruction of personal properties (t = 3.718 and 4.758, respectively, p < 0.001). Overall, males experienced more events than females (p < 0.001). The probable PTSD prevalence rates (29.1% among females and 31.9% among males) did not differ significantly (p = 0.212). Female IDPs reported more somatic (p < 0.001) and depressive/anxious (p < 0.001) symptoms than males. The demographic factors and duration of camp stay were not associated significantly with PTSD diagnosis. Probable PTSD rates among male and female IDPs in Iraq are substantial. Although no gender differences were found in probable PTSD rates between female and male Iraqi IDPs, the rate of common mental disorders cases was higher among females and they presented with higher levels of somatic and depressive/anxious symptoms. Further studies are needed to clarify the underlying mechanisms contributing to gender differences in PTSD.