FSU's ruling will be based on a "preponderance of evidence" -- a standard set forth in the "Dear Colleague" letter from the Education Department's Office for Civil Rights.
Two of Winston's teammates, Chris Casher and Ronald Darby, faced school code of conduct charges this summer. Only Casher, who told police he recorded the incident on his phone but later deleted it, was found responsible, and he received a year of probation, The Wall Street Journal reported.
Clune said he expects the university to charge Winston with violating the school's conduct policy.
"If somebody doesn't want to give his side of the story, I don't see how that could be the basis for not being charged," Clune said. "It's up to any student if they don't want to cooperate with an investigation, but it shouldn't work to their advantage to not give their side of what happened."
Florida State spokeswoman Browning Brooks declined to comment on the specific investigation, citing federal privacy laws, when contacted by USA Today.
"While we cannot comment on any individual case, in general, complainants control the timing in our process," she said.
Title IX suggests a school's investigation into any report of sexual misconduct should be completed within 60 days, but Florida State did not meet with Winston until January 2014, which was more than a year after the alleged assault.
Baine Kerr, another Title IX attorney representing the woman, told USA Today in April that FSU had suspended its investigation into Winston partly because he refused to cooperate.
Clune said it was "unfortunate" the university's investigation took so long to begin and after the woman already left Florida State, but he is "encouraged that they seem to be taking this seriously, and she'll certainly help with whatever they need."
Winston last season won the Heisman Trophy as a redshirt freshman and led the Seminoles to their first national championship since 1999.
Florida State currently is ranked No. 1 in both polls after starting its season with a 37-31 win against Oklahoma State.
Clune said he feels the football team's success has caused a "power struggle" within the university.
"I think the issue is there are definitely some people at this university that really want to do the right thing and want to comply with the law," Clune said in the interview with USA Today. "But it seems like there's a power struggle between those folks and people that would be just fine to just see this go away.
"We're dealing with one of the most powerful athletic departments in the country with the No. 1 football team in the nation, and I think we'll know very shortly how much control that athletic department has."
Winston did not talk with the Tallahassee Police Department or the state attorney's office during the criminal investigation. He said, through his attorney, that the sex was consensual.