The Selective Service and Transgendered People – Factsheet from the National Center for Transgender Equality (PDF)
Excerpt:
People who were assigned female at birth are not required to register with the Selective Service regardless of their current gender or transition status. When applying for federal financial aid, grants, and loans as a man, however, you may be asked to prove that you are exempt. The exemption letter you will receive does not specify why you are exempt so it will not force you to out yourself in any other application process. The Selective Service does, however, require a copy of your birth certificate showing your birth-assigned sex. If the sex on your birth certificate has been changed, attach any documentation you have to that effect. Once you receive your Status Information Letter, keep it in your files. For those FTM people who transition before their eighteenth birthdays and change their birth certificates, it is also possible to register with the service. However, no one may register after their twenty-sixth birthday. Also, please note that although Selective Service materials refer to transgender people as “people who have had a sex change,” their policies apply to those who have transitioned regardless of surgical history.
Specific instructions for transsexuals can be found on this page, under “Non-Citizen/Alien”:
The form has spaces for prior names and a special section for transsexuals where you list your birth gender. As mentioned above, although the Selective Service uses the term “transsexual,” this can include you even if you have not had surgery or transitioned physically, if your sex has been changed in public records, on your ID, etc.