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The aim of the current study was to compare the unified protocol for transdiagnostic treatment of emotional disorders (UP) with and without transcranial direct current stimulation (tDCS) for the treatment of emotion regulation and executive control dysfunction in individuals diagnosed with generalized anxiety disorder (GAD) and comorbid major depressive disorder (MDD). A total of 43 individuals with GAD and co‐morbid MDD were randomly assigned to three groups including UP with tDCS (UP+tDCS; n = 15), UP alone (UP; n = 13) or wait‐list control (n = 15). Difficulties in emotion regulation, reappraisal, suppression, inhibition and working memory were assessed at baseline, post‐treatment and 3‐month follow‐up. Treatment with both UP+tDCS and UP alone resulted in significant improvements in difficulties in emotion regulation, cognitive reappraisal, and working memory, and significant reductions in suppression and inhibition relative to wait‐list controls at post‐treatment and 3‐month follow‐up. Relative to UP alone, UP+tDCS showed significantly greater improvements in difficulties in emotion regulation, cognitive reappraisal, inhibition, and working memory at post‐treatment and 3‐month follow‐up. These results suggest combination of UP treatment with tDCS may be an efficacious intervention to improve emotion regulation and executive function in GAD with co‐morbid MDD. Trial registration reference is IRCT20140929019334N1 (see https://irct.ir/trial/27988).