The man, 65, was accused of two counts of sexually assaulting the five-year-old girl in 2009.

He had been to see a relative who was battling cancer and offered to look after the young girl while her mother and grandmother remained at the hospital.

As they drove home, it was alleged he told the girl they could share a secret and made explicit comments to her.

The Crown, represented by Shane Drumgold, alleged the abuse took place when they got home, in two different rooms.

It is the third time the man, who cannot be named, has been tried for the offences.

A jury couldn't reach a decision in the first trial, but he was convicted in the second and sentenced to eight years' imprisonment last year.

In both trials, the Crown relied on DNA evidence linking the accused to the girl's underwear to support her allegations.

He served 10 months behind bars but won an appeal and the right to a retrial after successfully arguing his counsel should have adduced evidence of his

The third trial took place in the ACT Supreme Court this week.

After further legal argument from the accused's barrister, Justice John Burns ruled the DNA evidence could not be admitted, leaving largely a word-on-word case.

It returned not guilty verdicts just after 2.30pm.

Speaking outside of court, a relative of the complainant said the family were absolutely devastated by the decision.

The relative, who cannot be named, said going through three trials had been traumatic, but was thankful the complainant got to have her voice heard.

"We've been to trial, this is the third time, we've had a hung jury, a guilty, and a not guilty," he said.

"It's absolutely traumatic ... but we do take comfort from the fact that we have listened to the victim in this instance."

The court experience was made distressing by lengthy delays and processes that forced the accused, his supporters, and supporters of the complainant to mingle, the relative said.

"It's a horrific and horrendous experience to have to go through, and I don't blame people for not wanting to go down that path, because it is so hard," he said.

"It has torn our family apart in so many ways."

The relative said the DNA evidence was crucial to the trial and found the decision to exclude it baffling.