Mbappé did not train with his teammates in Madrid's session at Valdebebas on Tuesday after suffering a muscular problem, and the club had delayed the announcement of the squad to face City, pending medical tests.
A source told ESPN that Mbappé had been pushing to be involved, but would not be 100% fit for the game, and it was yet to be determined if he would make the starting eleven or begin on the bench.
Mbappé has found the net 25 times in all competitions this season, with nine goals for Madrid in the Champions League.
The City game at the Bernabéu is a crucial test for Madrid coach Xabi Alonso, whose position has come under scrutiny after a run of one win in five games in LaLiga, including Sunday's 2-0 home defeat to Celta Vigo.
ESPN has reported that Madrid president Florentino Pérez met with club executives to discuss Alonso's future after the Celta loss.
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Mbappé scored four goals in Madrid's last Champions League outing, a 4-3 win at Olympiacos, as well as a hat trick against Kairat Almaty and two goals against Olympique Marseille, although he failed to score in games with Juventus and Liverpool.
Madrid are without seven other first-team players for the City game, including Dean Huijsen and Eduardo Camavinga, who were not included in the squad.
Éder Militão, David Alaba, Ferland Mendy, Dani Carvajal and Trent Alexander-Arnold are also missing for the clash.
