The 23 year old, who was intellectually disabled, disappeared while nine months' pregnant on June 20, 2009.
She discharged herself from Bendigo hospital and told friends she was going to a party in Pyramid Hill, but she never made it there.
Her family fears she was murdered by her unborn baby's father.
A Victorian inquest is investigating the circumstances leading to her disappearance and whether she was killed.
Ms Fraser's friend Nicholas Dingfelder told the inquest on Tuesday he had bumped into her on a train on the night of June 20.
They chatted about housing, he asked when she was due to give birth and she said she was being induced the next day.
The pair were getting off the train together at Pyramid Hill when Mr Dingfelder noticed a man walking on the train tracks about five or six metres from them.
"He had his hands in his pockets and he was kicking train rocks and I didn't think anything of it at first," he said.
"She said 'I've gotta get going, he's going to get angry at me'."
Ms Fraser went to meet the man, who Mr Dingfelder described as being stocky with short brown hair and sporting a fresh haircut.
He said the man seemed agitated and was well-dressed, wearing a black suede jacket, jeans and "looked like he had a bit of money".
He saw Ms Fraser walk away with the man across the train tracks towards the shops and did not see her again.
Mr Dingfelder said police showed him photographs of a number of men about a month ago and he identified one man that matched his description.
"I'm pretty confident that was the person I'd seen that night," he said.
He said police did not tell him the man's name.
The inquest heard earlier on Tuesday from Chantel Fraser, who said her sister was in a heated argument with a man named Peter Jenkinson in the weeks before she disappeared.
"He was pretty mad, he was screaming down the phone at her," she said.
"He was yelling at her, asked for the money, said 'come meet me', but she didn't go and meet him."
Ms Fraser told her family she did not know who the father of her child was but, she was considering doing a DNA test.
Several men have been named as possible fathers, including Mr Jenkinson and Gareth David.
On Monday, Mr David told the inquest he had never sex with Ms Fraser, despite telling police he had in 2009.
The inquest continues.
