Abstract Introduction Misunderstanding of different aspects of sex makes individuals vulnerable to sexual dysfunction, sexually transmitted diseases, mental disorders, and illegal relationships. This study aimed to determine the effect of cognitive behavioral counseling on the sexual self-concept of female students at Kerman University of Medical Sciences. Methods This study is an intervention conducted with female students living in dormitories at Kerman and Rafsanjan Universities of Medical Sciences. The sample size was estimated at 63 students from different fields of study; 31 students from Kerman University of Medical Sciences comprised the experimental group and 32 students from Rafsanjan University of Medical Sciences comprised the control group. Cognitive behavioral group counseling sessions were held every 3 days. The instrument used for collecting pre-test and post-test data was Snell’s Multidimensional Sexual Self-concept Questionnaire. Data analysis was conducted using measures of central tendency, t tests and chi-square tests. Results The two groups were homogenous in terms of demographic factors. Analysis of the results of the intervention revealed significant differences in sexual self-consciousness and motivation to avoid high risk sexual relationships, but there was no significant difference in terms of sexual depression. Discussion Cognitive behavioral group counseling can improve sexual self-concept. Therefore, this type of counseling is recommended from younger ages or at enrollment at university, to help correct development of this important part of identity.