BACKGROUND: The unified protocol (UP) is a promising transdisgnostic treatment for emotional disorders; limited data exists with trauma-exposed populations. This study compared effectiveness of the UP, presented centered therapy (PCT), and treatment as usual (TAU) in trauma-exposed veterans presenting to routine care. METHOD: Trauma-exposed veterans with one or more emotional disorder diagnoses participated in a pilot hybrid-1 effectiveness/preimplementation study. Thirty-seven male and female veterans were randomized to one of three conditions. RESULTS: Multilevel growth curve modeling demonstrated improvement over time across conditions with large effect sizes (range: -2.15 to -3.32), with the UP demonstrating the greatest change. The between group effect sizes for reductions in number of comorbid diagnoses were medium to small and statistically significant (TAU and UP, d = 0.49, p = .056; TAU and PCT d = 0.18, p = .166, UP and PCT d = 0.31, p = .229). Only the UP led to a decrease in the number of comorbid diagnoses (d = -0.71). Psychosocial functioning varied by group, with slight increases in impairment in PCT and TAU, and medium effect size reduction in the UP. Only the UP exhibited significant decreases in self-reported anxiety and depression. Between group differences for UP and PCT were medium to large and statistically significant for depression across two measures (d = -0.72 to d = -1.40). CONCLUSIONS: This represents the first trial examining effectiveness of the UP, PCT, and TAU in trauma-exposed veterans. Despite a small sample, large effect size differences demonstrated promising advantages for the UP. Trial Registration Number: NCT02944994.