Genito-Pelvic Pain/Penetration Disorder is a common sexual disorder that affects an individual's sexual health and overall well-being. Education is a therapeutic resource that presents several advantages, and it can potentially generate improvements both in pain and sexual functioning-related outcomes in patients suffering from this affliction. The objective of this study was to assess if a therapeutic educational program produced improvements in the different domains of the Female Sexual Function Index in participants suffering from Genito-Pelvic Pain Penetration Disorder. Participants were randomized into a group that received a face-to-face therapeutic educational program, a group that received the same program but online, or a control group. The Female Sexual Function Index was assessed, and analysis of the change in the domains for every group was performed using multiple t-tests. Improvements were found in the face-to-face intervention group, but only the "Pain" domain showed significant improvements (-1.1 points, p < 0.05). Improvements were also found in the online group, but they were only significant in the "Pain" and "Satisfaction" domains (-0.8 points, p < 0.05 for both). A therapeutic educational program improves pain-related outcomes, and it shows a positive tendency to also improve sexual functioning-related outcomes in patients suffering from Genito-Pelvic Pain/Penetration Disorder. Registration: Clinical Trials (NCT05114473).