Hayden injured his right leg against North Melbourne in his 100th game on Saturday and scans on Sunday revealed the break.
The 28-year-old saw an orthopaedic surgeon on return to Perth and underwent surgery on Tuesday.
General manager of football operations Chris Bond said it was initially thought Hayden had injured his calf.
“It was not until after Roger had scans on his leg and seen an orthopaedic surgeon yesterday that the full extent of the injury was able to be determined,” Bond said.
“Roger fractured the fibula in his leg and had a plate inserted during surgery today.
“Given the nature of the injury we expect at this stage that he will miss between six to eight weeks.”
Hayden missed the first three rounds of the season with a hamstring injury. But since returning he has been a key for Fremantle, playing important roles in the side's three wins.
Teammate Dean Solomon said the injury was devastating given how important Hayden was to Fremantle.
"Unfortunately he doesn't get the [same] exposure over east as what he does here," Solomon said.
"He's probably in the top five most important players at the club, just the way he plays and sets up our structure of play.
"He's going to be sorely missed, but no doubt he'll be back up and running in six weeks time and he can finish the year off with a month of footy and it'll set him up for next pre-season."
Solomon said Hayden's misfortune would grant an opportunity to one of Fremantle's many first and second-year players.
Rookie elevations Greg Broughton (two games) and Luke Pratt (one) have both been given chances in defence this season and would seem poised for a recall.
"We’ve got a lot of kids that we can get game time into and hopefully fast-track their level of skill or their anticipation of how the game is going to go," Solomon said.
"It'll hold them in good stead for next year or the year after if we can get a couple of games into them now."
