Albion have confirmed she sustained a ruptured anterior cruciate ligament injury playing for England against Australia on Tuesday.
The 19-year-old was introduced as a second-half substitute but went down clutching her knee.
Boss Sarina Wiegman said afterwards: “It was an awful moment, doesn’t look good. I’m not very positive about what I saw.”
Arsenal, Agyemang’s parent club, and Albion, where she is currently on loan, have now confirmed the bad news.
A statement from Albion read: “Michelle will miss the remainder of the season and we are in contact with her parent club Arsenal and will work together to determine a treatment and rehabilitation programme for Michelle.
“Everyone at Brighton sends all their support to Michelle as she begins her recovery, with her wellbeing foremost in all of our minds.”
The Gunners added: “We are in close contact with Brighton as we determine a treatment and recovery programme for Michelle.
“We send all our support to Michelle as she begins the road to recovery.”
Agyemang was one of the stars of this summer’s European Championship, scoring two vital equalisers in the knockout rounds to propel the Lionesses into the Basel final, where they successfully defended their title in a penalty shootout victory over Spain.
Albion captain Maisie Symonds said the injury was "a hard watch" as she followed the game on television.
Symonds told The Argus: "No matter what it is, we're going to do our very best to support her through it and she's still a very young player.
“She has come through lots of hard moments before already, high-pressure moments, and this is just maybe a new challenge for her but we will be there to support her.”
The injury leaves summer signing Carla Camacho, the former Real Madrid youngster, as the most likely spearhead of the Albion attack.
Dario Vidosic’s side face Manchester United at Broadfield Stadium this Sunday.