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Objectives: Posttraumatic stress disorder (PTSD) among female veterans is a problem of growing importance. Comparison of treatment outcomes and measures of program participation between female and male veterans receiving treatment in specialized intensive Veterans Health Administration (VHA) programs may identify potential gaps in service. Method: National program evaluation data were collected at program entry and 4 months after discharge. The study sample consists of N = 3,370 veterans who were successfully followed up. With adjustment for differences in baseline characteristics outcomes of women and men were compared on changes in PTSD symptoms, substance use, and other outcomes using Cohen’s d to evaluate effect sizes. Further analyses examined gender differences in program participation and their effect on differences in outcomes by gender. Results: Compared to males, females showed greater improvement (i.e., greater reduction) in total PTSD symptom scores (p < .001, Cohen’s d = −.29) and in several subscales including Numbness (p < .001, d = −.34), Arousal (p = .01, d = −.22), Reexperiencing Past Traumas (p < .01, d = −.23), and Irritability (p = .01, d = −.18), with small to medium effect size differences. These gender-based differences were partially explained by differences in program participation such as greater length of stay among women. Conclusions: In spite of the predominantly male environment of these VHA PTSD programs, women experienced greater improvement than men in PTSD symptoms and subscales. The differences were partially explained by positive indicators of program participation. Further studies are needed to better understand these differences.