The college says it allows a student to transition from female to male after being accepted, an issue that caused controversy last year last year when the administration did not allow male transgender students who were Gold Key tour guides to host high school applicants overnight in their dorm rooms.
"Smith seems to be saying they welcome trans men but not trans women," said Mara Keisling, executive director of the National Center for Transgender Equality.
"At its first blush, it appears to be counter to Smith's anti-discrimination policy," she said of Wong's application. "It doesn't make any sense.
"Smith College is one of the most prestigious women's colleges in the country and the primary purpose of a women's-only education is to really understand sex and gender," Keisling said. "So Smith really knows better than that."
The Free Application for Federal Student Aid, or FAFSA, is a federal form that can be filled out by the student, a parent or a guidance counselor and does not require official proof certifying gender.
Wong said her father filled out the FASFA forms, "according to what he thought was safest and most logical." He marked it male to match her Social Security information, which she said they had not yet had the chance to update.
"The crucial part about the campaign … is that Smith College used the FAFSA sex marker as a bar against processing my application," Wong said.
She argues that the sex marker on the FASFA form is only used for military Selective Service purposes. "The U.S. Department of Education does not cross-reference FAFSA sex markers with Social Security," she said. "Smith College would not be in any danger of losing federal funding as a historical women's college under Title IX."
Under federal law, Title IX bars discrimination against women in educational and sports programs.
"Though private colleges are legally permitted to reject applicants for any reason they want, private colleges are not allowed to simply refuse to process applications for any reason they want," Wong said. "Therefore, the FAFSA is irrelevant and should not be used as an arbitrary bar against even processing my application."
Wong, who attends Amity Regional Senior High School in Woodbridge, wrote about Smith's policies in her blog on Tumblr while exploring options at the college last summer.
She said she will not appeal again to Smith for admission.
"However, this does not mean that I am in any way giving up on my cause," Wong said. "I continue working so that others who care about equal rights have access to the truth. And, most importantly, I do this for the transfolk after me, so that they might inherit better policies and a more just system of education."
Wong said she had gained the "overwhelming" support of numerous Smith students and alumni, including the chair of diversity at the college.
A faculty member confirmed that many student groups had been in touch with Wong and were involved in an "ongoing" debate with the administration.
Some students argue that it is also has a "class impact," she said, when those who cannot afford a Smith education must fill out the federal FASFA form for financial aid.
But Wong has also received negative responses.
"The lack of visibility -- marginalization -- is the root of all social problems for not only me, but all transfolk in society," she said. "Every time I fill out paperwork with sex options of male or female -- get stared at while walking in public -- I feel like the world doesn't yet understand."