North Australian Aboriginal Legal Aid Service (NAALAS) principal lawyer Glen Dooley has confirmed an application had been lodged with the High Court on behalf of the 55-year-old man, who is currently in jail.
"We have lodged an appeal with the High Court, we are seeking leave to appeal," Mr Dooley said.
The case last year flamed debate about the role of customary Aboriginal law in the wider Australian legal system, as the traditional Aboriginal man believed his actions were allowed under tribal law.
The man, who speaks English as his fourth language and lived in the remote Northern Territory (NT) outback, also did not know his actions were illegal under territory laws. His name is suppressed to protect the victim.
The court had heard the girl was promised to the man when she was just four.
He became angry after she struck up a friendship with a young man during her school holidays last June.
Believing the girl had a sexual relationship with the boy, the man beat her with a boomerang at the outback Aboriginal community, south-west of the town of Katherine.
He later took her to the remote outstation where he lived with his wife and young children, threatened her with a boomerang and had anal sex with her.
In August last year, the man pleaded guilty to one count of aggravated assault and one count of carnal knowledge, and received a two-year sentence suspended after one month.
The Director of Public Prosecutions appealed the leniency of the sentence in the NT Court of Criminal Appeal, which found the sentence "manifestly inadequate".
In December, the court imposed a total sentence of three years and 11 months, suspended after 18 months.
Mr Dooley said NAALAS was seeking to appeal on several grounds, including that the appeal court based some of its decision on an apparent lack of contrition, even though the man believed his actions were acceptable under Aboriginal customary law.
Nor did the court place enough weight on the man's personal factors, such as his age or lack of prior convictions, he said.
"He has been asked to carry a lot of this community education through his jail sentence," Mr Dooley said.