Background: There is a lack of research on the sexual health of transgender individuals, as well as a paucity of data about overall sexual health indexes before treatment. Aims: This study aims to analyze the main issues involved in transgender individuals' sexual behavior (with and without a partner), overall sexual health indexes, and potential predictors of sexual health, comparing trans men and trans women on all the variables assessed. Methods: 260 trans people were recruited at a transgender health clinic in Spain. Participants completed the Sexual Behavior Questionnaire for transgender people before receiving any treatment. Results: Overall results show that trans women have a more ego-dystonic and problematic experience of their sexuality. Regarding masturbation, there are no differences in its frequency between trans women and trans men, although there are differences in the reasons they do not masturbate. Regarding sexual behavior with a partner, trans women experience more difficulties than trans men, with significant differences in several areas (e.g., the percentage of transgender individuals who never allow their partners to touch their genitals). Regarding sexual health, we found differences between groups, with lower sexual desire, sexual arousal without orgasm, and overall sexual health in trans women. Likewise, different variables such as pain during sex, fantasies, and time with a steady partner seem to be associated with the different sexual health indexes. Conclusion: Our results show a clear difference between trans women and trans men in most of the sexual aspects assessed, revealing greater gender dysphoria in trans women. We would recommend taking these data into account, as well as variables that may be associated with different sexual health indexes, when designing interventions for transgender people.