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Zirkzee limped off during the 4-1 loss to Newcastle last weekend and appeared very upset as he was helped off the field.
"He is out for the season," Amorim said in his press conference before the second leg of the Europa League quarter-final against Lyon on Thursday. "He won't play again this season, so let's focus on getting him ready for next season.
"It's tough; he was improving in every part of his game. It's hard for any player, but he needs to be ready to recover."
Amorim also shared that Andre Onana will return to the starting lineup for the match against Lyon. The goalkeeper was benched after a poor performance in the first leg against the French team and had a public dispute with Lyon midfielder and former United player Nemanja Matic.
However, Altay Bayindir also struggled, conceding four goals against Newcastle, which means Onana will take back the No. 1 spot on Thursday.