The youngster will see a specialist next week to assess whether he needs surgery on the injury, picked up ion Saturday's 1-1 draw with Bolton.
But there was better news on Wednesday’s lengthy injury list today, with Barry Bannan, Sam Hutchinson and Joost van Aken all in contention to return for Saturday’s trip to Leeds United.
“Joost van Aken, Sam Hutchinson and Barry Bannan are training 100 per cent with the team,” confirmed Owls manager Jos Luhukay.
“Sam and Joost have played with the Under-23s, they are in a very good shape.
“They have done a lot of work in the last week, so they are options for Saturday.
“They are 100 per cent and I am very happy to have options in my squad. I have three options for my squad, and maybe my first XI.”
Owls rookie Clare, 21, was drafted in because of the depleted first-team squad, and has impressed many at S6 in his five appearances in 2018.
“Yesterday we had a shock moment, Sean Clare is out for the rest of the season,” added Luhukay.
“Last Saturday he hurt his ankle, and next week he must see a professor and decide whether he needs surgery. That will depend then on how long he is out.
“You can say he will not play again this season.”