The 23-year-old was sidelined from late September until December last year with a troublesome groin injury but had fought back to fitness following the arrival of Shaun Maloney.
Magennis was on the verge of returning to the Easter Road matchday squad in late January, with a return pencilled in for the Livingston game on January 29, but a knee injury sustained in a bounce game led to a further setback and the former St Mirren man added to Maloney’s injury concerns.
The Hibs manager said last week that the club would likely know more about the midfielder’s situation early this week, and the player himself has confirmed that he will be out of action until the new season.
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Posting a photo from a hospital bed showing his left knee, Magennis wrote: “Gutted my season is over but surgery went well, back for pre-season.”
Magennis has been a big miss for Hibs after starting the season in fine form, scoring four goals and laying on two more in just 13 games.
Maloney had been hopeful that he would return to training after the international break, telling the Evening News: “I'm really hopeful that he can come back within two or three weeks of the break because what I saw of him in training, I really liked.
"It's hard because he was so close and before the bounce game, I was definitely ready to put him in the squad.
"To have that setback can be hard mentally but we look forward to having Kyle back. Even what I saw when I analysed the team before coming here, he stood out as a really strong runner from midfield with a big goal threat, and that’s certainly something we've missed from that area of the pitch.”
Harry Clarke made his debut for Hibs on Saturday, scoring in the 1-1 draw with Dundee United. But seven first-team players missed out with Matt Macey, Paul McGinn, Demi Mitchell, Christian Doidge, and Kevin Nisbet all injured and Ryan Porteous serving the first of a four-game suspension.