Abstract Background Cancer survivors frequently develop cognitive impairment, which negatively affects their quality of life and emotional well-being. This study compares the effectiveness of a well-established treatment (neuropsychological treatment) with the Unified Protocol for Transdiagnostic Treatment of Emotional Disorders (UP) to reduce these cognitive deficits and evaluate the effect of both treatments on anxiety-depressive symptoms and the quality of life of cancer survivors. Methods A three-arm, randomized superiority clinical trial with a pre-post and repeated follow-up measures intergroup design using a 1:1:1 allocation ratio will be performed. One hundred and twenty-three cancer survivors with mild to moderate cognitive impairment will be randomly assigned to one of the study interventions: a cognitive rehabilitation intervention group, an intervention group with UP intervention, or a control group on the waiting list. The primary outcome is to observe a significant improvement in cognitive function in both intervention groups and a significant decrease in emotional impairments in comparison with the waitlist group. Improvements in anxiety, depression, and quality of life are also expected as secondary outcomes. These results will be maintained at 6 months of follow-up. Discussion The aim of this trial is to test the efficacy of the UP intervention in reducing cognitive deficits in breast cancer survivors. The results of this trial may be useful in reducing the presence of cognitive problems in cancer survivors and improving their emotional state and quality of life. Trial registration ClinicalTrials.gov NCT05289258. Registered 12 March 2022, v01.