Thomas became the first transgender NCAA champion in Division I history after winning the women's 500-yard freestyle in March.
She had hoped to compete for a place at the Olympics but soon became the focus of a heated debate.
Swimming's world governing body FINA voted last month to restrict the participation of transgender athletes in elite women's competitions.
Thomas competed on Pennsylvania's men's team for three years before transitioning and moving to the women's team, setting multiple programme records.
Her eligibility had come under considerable scrutiny, including from several Pennsylvania team mates.
The NCAA said member schools nominated a total of 577 graduating student-athletes.
Each school can recognise up to two female athletes and Thomas had been nominated for swimming and diving in Division I.
The Woman of the Year selection committee will select 10 student-athletes from each of the three NCAA divisions.
Of the top 30, the committee will then announce nine finalists — three from each division.
The winner will be named at the NCAA Convention in January in San Antonio.
It comes after Thomas was accused of "cheating" to win an NCAA swimming title, by Lord Daniel Moylan.
Appearing on GB News, Lord Moylan slammed the decision to allow Thomas to compete in the event.
He said: “It’s cheating, that’s what it is, it’s a form of cheating."
When asked how it can be cheating if the rules allow it, he told Dewbs & Co: “Because the rules have been written so as to allow cheating and they’ve been written that way because sports bodies have been ideologised, bullied, harassed, taken over by people who hold this view as a matter of ideological belief.”
Lia Thomas
Brett Davis
Lia Thomas swims the 100 free at the NCAA Swimming & Diving Championships at Georgia Tech
Brett Davis