People with epilepsy (PWE) are highly likely to suffer from sexual dysfunction, and dealing with this issue is a challenge for healthcare providers. Unfortunately, there is no theory-driven study that has investigated the counseling practice of healthcare providers for sexual problems in PWE. Therefore, we decided to apply the well-established Theory of Planned Behavior (TPB) to examine factors associated with healthcare providers' sexual counseling in PWE. Apart from TPB, perceived barriers toward providing counseling could be a possible factor that needs to be investigated as well. Therefore, two models explaining sexual counseling practice were proposed. Model 1 included only TPB and Model 2 included TPB incorporated with perceived barriers. Five hundred fifty-nine Iranian healthcare professionals responsible for PWE were recruited across several neurology clinics and asked to complete TPB-specific questionnaires. The same healthcare professionals were asked to complete an additional questionnaire on their attitudes toward sexual counseling 18months later. Structural equation modeling suggested Model 2 to be more useful in explaining sexual counseling practice compared with Model 1. Moreover, attitude and perceived behavioral control showed stronger associations with behavioral intention, whereas subjective norm showed weaker associations. The associations were similar across different healthcare professionals (i.e., medical doctors vs. nurses). In conclusion, TPB incorporated with perceived barriers might be a useful theory for different types of healthcare providers to improve and enhance sexual counseling practice.