Domaine Javier, 25, was expelled from the private Christian school in August 2011 after she appeared on an episode of an MTV show called "True Life" to discuss the stigma experienced by transgender people. She revealed that she was biologically male.
Javier came to the U.S. from the Philippines in 2007 and says she has viewed and presented herself as female for as long as she can remember.
The lawsuit alleges that Javier's civil rights were violated because she was expelled on account of her gender identity. She was informed that she violated the university's policy against "committing or attempting to engage in fraud or concealing identity" because she stated on her admissions application that she was female.
"Ms. Javier honestly answered the questions contained in the admissions application," said her attorney Paul Southwick. "CBU is a religiously affiliated university, but it is open to the public and it does not require its students to be Christian."
The Superior Court suit seeks $500,000 damages. University lawyer Theodore Stream refused to comment on the suit, saying he hasn't seen it.
The Associated Press contributed to this report.