A tenacious aunt helped find missing Melbourne teenager Owen Clune who had not been seen by friends or family since he left for school on Tuesday morning.

The 14-year-old was found this morning at Caulfield Railway Station after he went there to meet police and his aunt Megan.

Owen's mother Bronwen Clune, a journalist who works between Melbourne and San Francisco, tweeted that her sister Megan followed the trail last night when the family noticed Owen accessing his voice mail.

"We noticed last night that he was accessing voice messages his sister was sending him. We all kept sending him more," Clune tweeted.

"My sister Megan was out all night and didn't give up, sending him a message every 15 and telling him she'd see him at Caulfield station.

"After about 5 hours he sent a message back saying he would see her there. We're really happy to have him home. Thanks again x"

Earlier the grateful mother used Twitter to thank everyone for their help.

"Everyone has been so amazing and I want to thank everybody for their support in helping find Owen."

Clune later tweeted that the family was enjoying McDonald's breakfast but there has not yet been an explanation about where Owen was over the past three days.

Victoria Police announced early this morning that Owen was found "safe and well" after they met him in Caulfield.

"My son Owen is safe and with us. I'm going in for a bear hug," Clune tweeted.

Owen Clune had not been seen since he left his home in Thornbury Crescent in Malvern East at 8am on Tuesday.

Owen's father said he was relived at the news when it came through early this morning.

"We hadn't been getting any sleep and when the call came through it was just a huge relief.

"When we saw him we just wanted to make sure he was good and it was surprisingly normal to see him again."

His mother rushed home from San Francisco, using Twitter to urge anyone with information about her son's whereabouts to come forward.

"He's obviously upset about something, so we're worried on a number of fronts as to how he is," she said.

"Just want to find him and make sure that he's okay, no one's angry at him, he's not in trouble.

"Just want to find him and bring him home safely."

A digital editor and journalist and prolific tweeter, Clune used Twitter to ask for assistance finding her son.

"If there's somewhere a kid might seek shelter near you in pouring rain — please take a look. We need to find Owen," she wrote.