The Spain international tore the anterior cruciate ligament in his left knee during Saturday’s 2-0 defeat at Sevilla.
Muniain will go under the knife later this week and is expected to be sidelined for at least six months.
“Unfortunately, the worst prognosis was confirmed,” Muniain wrote on his Instagram account. “I will be several months without doing what I love, which is to play football.
“It’s a big blow but I’m ready to combat this injury, recover well and return to the pitch much stronger than before.
“I don’t forget that in life there are worse things than a knee injury.”
Muniain, 22, will miss his team’s next nine Primera Division games as well as the Copa del Rey final against Barcelona on May 30.
“I’m sad for the injury but happy to see so many people giving me support,” he said.
“This will no doubt give me further strength.
“I want to thank all of the fans for all the messages of support.”
Muniain has started in 25 league games for the Basque outfit.
Athletic are eighth in La Liga and host Valencia on Thursday.