Mary Willingham said in an email to The Associated Press on Monday night that she met with Chancellor Carol Folt earlier in the day.
Willingham says in the email that she and Folt "clearly have different ideas and opinions."
"She has a job to do and I hope that she does the right thing -- academics should be in charge of this great university, not athletics," Willingham said.
She says she will meet with her supervisor after she posts her grades next week to submit her letter of resignation and finalize details.
Willingham told CNN in January that her research of 183 football or basketball players from 2004 to '12 found 60 percent reading at fourth- to eighth-grade levels and roughly 10 percent below a third-grade level.
Three outside experts hired by UNC issued reports earlier this month saying Willingham's research data doesn't support her claims. One of them estimated about 7 percent of athletes from Willingham's research read at fourth- to eighth-grade levels.
The school said the data included scores for 176 athletes, including baseball and volleyball players, and was based on testing to screen for learning disabilities or other problems.
The school said it had about 1,800 athletes attend the school during the eight-year period.
UNC had called Willingham's findings flawed after its own internal review of her data, which she provided to Provost James W. Dean Jr. She has stood by her findings.
Willingham met last week with former U.S. Justice Department official Kenneth Wainstein, who was hired by UNC to conduct a review of possible fraud in the formerly named African and Afro-American Studies Department.
The alleged irregularities, dating to the 1990s, included lecture classes with significant athlete enrollments that didn't meet and were instead treated as independent studies requiring only a research paper.
Willingham has said those "paper classes" were designed to keep athletes academically eligible to remain in school.
Wainstein's investigation is the latest to look into the possible AFAM fraud. One conducted by former Gov. Jim Martin in 2012 assigned blame to former department chairman Julius Nyang'oro and retired administrator Deborah Crowder. Nyang'oro has been indicted and is accused of being paid $12,000 to teach one of the paper classes filled with football players in the summer of 2011.
The attorney for Crowder said his client met with Wainstein on March 19. Crowder hadn't cooperated with earlier investigations, and has not spoken publicly since the investigations began.
It was unclear when Wainstein would complete his investigation.
UNC Academic Scandal: Whistleblower, Former Athlete Speak Out
North Carolina whistleblower Mary Willingham and former football player Deunta Williams discuss the fake classes that student-athletes were allegedly encouraged to take in order to maintain eligibility to play.
North Carolina Academic Scandal
Dr. Deborah Stroman, Chair of the Carolina Black Caucus on UNC's campus, and Phillip Jackson, executive director of the Black Star Project, discuss the allegations of academic fraud at the University of North Carolina-Chapel Hill.