Schoenmakers went down during the second quarter and was immediately subbed out of the game.
Scans have confirmed that Schoenmakers has ruptured the anterior cruciate ligament and will require a reconstruction.
Hawthorn's general manager football operations, James Fantasia, said Schoenmakers was understandably devastated by the news.
“While Ryan is naturally disappointed by the injury, we’re certain he will approach his rehabilitation with the same professionalism, positivity and dedication he has displayed as a young player,” Fantasia said.
Schoenmakers will consult with a specialist in coming days.
"Whenever a player goes out with an injury where he lands awkwardly like that, it's probably unlikely to be good," Hawthorn coach Alastair Clarkson said after the game.
"We just have to hope for the best. Usually the docs aren't too inaccurate on some of these calls, and we're not overly confident that he'll be playing for the rest of the year.
"(They think) he has some damage there that will keep him out for a long period of time.
"That's footy. You have to roll with the punches on these sorts of things.
In a twist of fate, Schoenmakers was hurt in the same spot that his teammate Matthew Suckling suffered a season-ending knee injury during the NAB Cup.
Schoenmakers is the third Hawk to tear an anterior cruciate ligament in 2013.
Suckling and Alex Woodward are already out for the season, while Brendan Whitecross is fighting back after suffering a similar fate during last year's finals series.
Schoenmakers' travails will most likely pave the way for star recruit Brian Lake to play his first game for the Hawks when they take on North Melbourne at the MCG next weekend.
"Lakey was really close to playing today and probably would have had the Pavlich thing not been announced," Clarkson added.
"We'll just wait and see. Lakey is an important part of our back mix and it's not like he can't get a game.
"We're just making sure he's absolutely match-fit before we need to use him."
There were no such injury concerns for Fremantle, but coach Ross Lyon was left scratching his head after his men allowed Hawthorn to kick five unanswered goals in the first quarter.
"Hawthorn jumped us out of the blocks," Lyon said. "Can't ignore the start – really disappointing.
"I thought they were really dominant all over the ground in all areas."
Freo fought back early in the last term, but Lyon's men faded late, with the Hawks booting the last four goals of the match.
"So we really gathered ourselves, changed a few things at the break, and I thought we really fought on really well," Lyon said.
"We got to 17 points and we had some opportunities that we butchered to be a bit closer and really put some pressure on.
"Then at the end, trying to push the envelope, we opened ourselves up at the back end and it blew out a little bit more again, but that didn't sort of worry me.
But after that I thought there was some really good character and some good method.
"(There was)a little bit of a lack of class at times to finish the job when we'd worked hard."
Fremantle appeared to dearly miss the input of skipper Matthew Pavlich, who will be sidelined for six weeks after having Achilles surgery, and defender Luke McPharlin, who was a late withdrawal after failing a concussion test.
But an agitated Lyon refused to use those key absentees as an excuse.
"In all honesty, it was irrelevant," he said. "I think we unearthed an exciting young tall defender today in Tanner Smith. Under real pressure, I thought he stood up.
"They're big men, Hale, Roughead, Franklin. They're as big power forwards as you're going to get as a combination.
"He's big boy, a great athlete and a fierce competitor, so we think he's got real upside.
"McPharlin and Johnson and Dawson will mentor him, grow him, to he a good key defender for us."
McPharlin is likely to return for Freo's clash with Richmond at Patersons Stadium on Friday night.
"If he had passed the test he would have played today, so he had the test as late as today. So we're hopeful."