Objective: This study aims to test the mediation role of sexually-related thoughts on the relationship between sexual functioning and pain intensity in men with genital pain. Design and Method: A total of 50 men with genital pain completed an online survey. Participants answered the automatic thoughts subscale of the Sexual Modes Questionnaire (Male Version), the International Index of Erectile Function and the McGill Pain Questionnaire (the Short Form). Mediation analysis was conducted through linear regression equations. A Sobel test was used to assess the significance of the mediation effect. Results: In Step 1, the regression of sexual functioning on the mediator was significant, β = -.68, t(50) = -5.8, p <.001. Step 2 showed that the regression of sexual functioning on pain intensity was also significant, β = -.39, t(50) = -2.6, p =.014. Step 3 showed a significant effect of the mediator on the pain intensity, β = .68, t(50) = 3.8, p =.001. Also, sexual functioning was no longer a significant predictor of pain intensity, β = .06, t(50) = .37, p =.711. Additionally, the Sobel test found a partial mediation effect (z = 2.37, p = .018). Conclusions: Findings showed that negative sexually-related thoughts partially mediated the relationship between sexual functioning and pain intensity in men with genital pain. Results are consistent with previous research and reinforce the use of cognitive techniques in the evaluation and treatment of male genital pain.