Background: During the menopausal transition, women often experience physical (e.g., vasomotor symptoms) and emotional (e.g., anxiety and depression) difficulties that significantly impact functioning and overall quality of life. Although sexual concerns (e.g., decreased sexual desire, orgasm), are reported by up to 87% of peri- and post-menopausal women, and are associated with adverse impact on functioning and distress, treatment options that directly target this area are limited, and most often involve medication (e.g., hormone replacement). Effectiveness of these treatments is often defined as improvements in physical symptoms, however, associated psychological and emotional symptoms rarely, if at all, improve. Cognitive behavioral therapy (CBT) has been proposed as a low-risk treatment for menopausal symptoms with studies showing improvement in frequently reported symptoms (e.g., vasomotor symptoms, depression, anxiety, sleep). Sexual concerns, however, have either not been directly targeted at all in current CBT protocols, or the very few protocols that include sexual concerns, demonstrated modest gains in sexual desire.Methods: This protocol paper outlines the development, design, and implementation of a newly developed CBT for sexual concerns trial during perimenopause (CBT-SC-Peri). Although sexual concerns are prevalent during both the peri- and post-menopausal periods, we will be evaluating the effectiveness of a CBT-SC protocol specifically for perimenopausal women as a means of early intervention. The clinical sample will comprise 82 women aged 40–60 years currently in perimenopause, as per the Stages of Reproductive Aging Workshop (STRAW) definition, and medication stable (if applicable). To ensure participants are experiencing clinically significant sexual concerns, a baseline cut-off score of 26 or lower on the Female Sexual Functioning Index will be utilized. Exclusion criteria include participants with psychotic disorders, or current substance and/or alcohol dependence, or severely depressed/suicidal. The CBT-SC-Peri is a weekly, four session treatment, lasting up to 90 min per session and includes psychoeducation and cognitive and behavioral strategies designed to challenge unhelpful beliefs and promote healthy sexual behaviors. As this is an individual CBT protocol, content will be tailored to address the specific problems relevant for each participant. Eligible women will be placed directly into treatment or on a 4-week waitlist and reassessed prior to starting treatment. The primary outcome (sexual satisfaction), as well as secondary outcomes (desire, arousal, relationship satisfaction, body image, vasomotor symptoms, depression, and anxiety) are assessed at baseline, post-waitlist (for those on waitlist), and post-treatment.Discussion: To our knowledge, this will be the first study to investigate the efficacy of a CBT protocol (CBT-SC-Peri) specifically aimed at improving sexual concerns experienced during perimenopause. If effective, this form of treatment may not only be preferred by some, but necessary for others as consumer demand increases for non-pharmacological treatments for perimenopausal symptoms. Further, this protocol can be integrated into perimenopausal care and will be made available by dissemination to healthcare practitioners.Clinical Trial Registration: Trial # NCT04922385 and Accessible at: https://clinicaltrials.gov/ct2/show/NCT04922385?term=NCT04922385anddraw=2andrank=1.