Thomas, 23, is expected to front the AFLIU at league headquarters on Thursday.
"North Melbourne received notification from the AFL Integrity Unit on Wednesday that Tarryn Thomas is under investigation following a new allegation of inappropriate behaviour," the Kangaroos said in a statement.
"The club is working through this information and is not in a position to make any further comment."
AFL spokesperson Jay Allen also confirmed the AFLIU were investigating.
Thomas, who is out of contract at the end of the 2024 season, was stood down by North Melbourne twice last year, first in February and then March, amid concerns over his behaviour towards women.
Thomas was put through a respect and responsibility education program and spent three weeks in the VFL before later earning a senior recall, ultimately playing 12 AFL games last year.
When he returned to the VFL program, chief executive Jennifer Watt said the club had "made it clear to Tarryn that the future of his playing career at North Melbourne is in his hands."
In July, Thomas walked free from court without a criminal conviction for threatening to distribute intimate videos of his former partner.
He was initially charged with threatening to distribute an intimate image of another person, but this was downgraded by prosecutors to using a carriage service to harass someone.
Thomas was granted a diversion, which meant he escaped a criminal conviction, and was ordered to pay $1000 to charity.
The midfielder, drafted at pick No. 8 in the 2018 national draft, has played 69 games and kicked 56 goals in a career interrupted by injuries and off-field issues since his 2019 debut.
That included kicking 11 goals in 12 appearances last year, when he finished sixth in North Melbourne's best and fairest despite limited games.
Thomas underwent groin surgery late last year and has been gradually returning to training.
The news came a day after co-captain Jy Simpkin tipped his teammate to thrive in the upcoming season.
"He had a really good off-season. He knuckled down, he had a bit of a groin interruption unfortunately," Simpkin told reporters on Tuesday.
"But he's working hard, he's in a great mindset at the moment so can't wait to see what he does this season."
