Calliope Wong, 17, was born a male and that's what her family indicated on her federal form for financial aid, ABC News reported.
However, all the admissions material she submitted to prestigious Smith College indicates she is a female.
Smith has twice told her it can't process her application because the gender markers on those forms conflict.
"Someone whose paperwork consistently reflects female identity will be considered for admission," said Laurie Fenlason, Smith's vice president for public affairs.
The college said it allows a student to transition from female to male after being accepted and Wong is free to reapply.
Mara Keisling, executive director of the National Center for Transgender Equality, said Smith seems to be saying it welcomes "trans men but not trans women."