Bumble Bees worker Lucas Jacob Garratt allegedly abused the girl multiple times while babysitting her in her Border home on August 28 last year.

He had looked after the alleged victim through the childcare centre and had babysat her family since December 2017.

He no longer works at Bumble Bees.

The girl's mother became distressed in the Wodonga Magistrates Court as she recalled her daughter coming to her the morning after the alleged incidents.

"Why did Lucas lick my vagina?" the girl allegedly asked.

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"I don't understand why he was doing it.

"It was strange."

Her mother asked her to repeat what she said and hugged her daughter.

"I didn't know what I'd heard," the woman told the court.

The mother said she had "screamed" out to her husband to come to her and they recorded their daughter on a phone two or three minutes later.

Contact was made with police.

The recording was given to sex offence investigators and the girl was interviewed twice.

A forensic medical evidence kit was used at Albury hospital.

Her underwear and pyjamas were seized as evidence from her home on August 30.

The court heard her underwear allegedly contained Garratt's DNA.

The court heard Garratt allegedly went in and out of the girl's room three times during the night and abused her each time.

Her parents had known Garratt for several years.

He has entered not guilty pleas on six charges, including that he sexually penetrated a child under 12 with his finger and tongue, and sexual touching "contrary to community standards of acceptable conduct".

The charges were filed by a sex offence detective on February 11 following an investigation.

The mother said her daughter and another child had attended Bumble Bees while Garratt worked there.

The court heard Garratt, aged in his mid-20s, had been "very good with kids".

The girl frequently goes to her parents to talk about what allegedly occurred.

Detective Leading Senior Constable Dave Bruce said it had been a very short investigation given the small number of witnesses.

The court heard the girl denied some of her earlier claims during a video and audio recorded interview at the Wodonga Police Station.

Investigators later spoke to her parents about receiving counselling from the Centre Against Violence.

Magistrate David Faram ordered Garratt to stand trial, and he pleaded not guilty.

The matter will return to the county court on July 8 for a directions hearing.