The Nigeria midfielder limped off in his side's 2-1 second-leg defeat by Rennes in the Europa Conference League earlier this month.
Ndidi, 25, has since undergone surgery and will be sidelined for the run-in.
Leicester boss Brendan Rodgers said: "Wilfred Ndidi will be out for the season, it's a shame for us, but he'll get ready for next season."
Ndidi had also been ruled out of this week's World Cup qualifiers for Nigeria, who failed to progress to the finals in Qatar after drawing with Ghana in their play-off.
"It's unfortunate," added Rodgers. "He's been a brilliant player for me in my time here. He picked up a nasty injury that has had to have surgery on and he'll recover now until June."
