Kevin Henry O'Rafferty, 43 and his co-offender Jason Heath Dodd, 41, were convicted in June last year of sexually assaulting a 16-year-old as she lay in Dodd's Stuart Flats unit in the early hours of May 18, 2012.

The teenage victim had gone to Mr Dodd's place with a friend, and the pair were drinking.

She gave evidence that she fell asleep on the couch, but woke in the early hours of the morning to find some of her clothes removed, and Dodd and O'Rafferty sexually assaulting her.

She said she blacked out and woke again to find the assault continuing.

The young woman woke in a bedroom later that morning and left in distress.

Dodd and O'Rafferty both faced a jury trial before the ACT Supreme Court in June last year.

There was no DNA evidence linking O'Rafferty to the crime, and some evidence suggested he left the flat and wasn't present at the time of the assault.

O'Rafferty was found guilty of one count of sexual intercourse without consent and sentenced to a maximum of five years imprisonment.

But he appealed his conviction, arguing the trial judge Acting Justice John Nield had failed to fairly put his case to the jury.

He also argued Justice Nield's directions to the jury about the victim's evidence of complaining to others about the assault gave rise to a miscarriage of justice.

The judge, his lawyers argued, also failed to direct the jury about the dangers of identification evidence.

The ACT Court of Appeal upheld the appeal on Thursday, setting aside O'Rafferty's conviction, and ordering a new trial.

"The case put on behalf of Mr O'Rafferty was not adequately put to the jury by the trial judge," the judges wrote.

"Indeed we think the problem is compounded by the fact that the trial judge suggested that, save in one respect, the complainant's accounts were consistent."

"Significantly his honour did not put the other alternative to the jury - that Mr O'Rafferty was present but did not sexually assault the complainant."

That, the full bench found, deprived O'Rafferty of a real chance of acquittal and led to a miscarriage of justice.

O'Rafferty was given bail and will face a second trial later this year.