The livewire forward was the only inclusion to the team, with young midfielder Cam Sutcliffe the player to make way.
The emergencies for the match are Tom Sheridan, Alex Silvagni and Sutcliffe.
See both Fremantle and Carlton line-ups here.
Freo assistant and senior development coach Simon Lloyd said the club welcomed Ballantyne back after two weeks on the sidelines with a hamstring injury.
“Hayden is a very important player for us and to have him combining with Michael Walters up forward at Etihad Stadium, it’s going to be exciting,” he said.
Lloyd said Sutcliffe had made a solid contribution to the senior side all season and was unlucky to miss out.
“He needs to just keep doing to what he’s been doing,” Lloyd said.
“He’s a tremendous runner and a great ball getter. Cam’s getting more and more confident with the more football he’s playing.”
With Carlton power forward Jarrad Waite still out injured, Fremantle chose not to select key defender Silvagni, despite the absence of regular full-back Luke McPharlin.
Lloyd said the club had a number of players capable of performing roles in defence, with those playing on Carlton’s fleet of skilful small forwards of particular importance.
“We’ve had different players at different times, like Tendai Mzungu and Clancee Pearce, who have been able to go back,” he said.
“We’ve got a versatile team that can play in defence and we’re going to need that this week with (opposition) players like Eddie Betts, Jeff Garlett and Chris Yarran, who are all very, very quick, and Marc Murphy has been going through the forward line as well.”
Fremantle senior coach Ross Lyon labelled the 9th-placed Blues as good as any side in the competition at their best, and Lloyd agreed.
He highlighted the strong form of Carlton’s midfield as a key reason behind three wins in succession for Mick Malthouse’s side.
“Between (Matthew) Kreuzer, (Chris) Judd, Murphy and (Mitch) Robinson, they’re really starting to get going as a midfield group,” he said.
“They are quite potent and they’ve got a great tall target in Henderson, who kicked four last week.
“With the small forwards, they like to try and get you out the back, so they’re dangerous.”
