Real will have four days to prepare for the clash at the Bernabeu after their La Liga game at Real Sociedad on Saturday and Pellegrini thinks City’s game should have been brought forward to correspond.
The club made enquiries as to whether that was possible, but it is understood an official request was not submitted as it was felt it would be unlikely to succeed for a televised fixture.
“For me it is unbelievable,” said Pellegrini, whose side will have all to play for in Spain after a goalless draw in the first leg at the Etihad Stadium.
“If you see other leagues, including Italy, the teams that play Champions League play their domestic games on a Friday.
“We are representing England and I think it’s important not to give any advantage to the other team.”
It is the second time this season City have been frustrated by fixture scheduling ahead of a European game.
The first leg of their last-16 tie at Dynamo Kiev came three days after their FA Cup fifth-round clash at Chelsea. City were angry that a request to have that game moved failed and they consequently fielded an under-strength side at Stamford Bridge.
That will not happen in this instance as City need points to tighten their grip on a top-four spot in the Premier League, but Pellegrini is likely to make changes.
The Chilean said: “In the Premier League, I don’t understand why, when having so many games, and they all have the same interest, we can’t play one day before to have 24 hours (more rest), at least having the same as Real Madrid.
“We knew we had to play eight games in 30 days. It is a lot of games for this squad, so I am making rotations in every game, and changes.
“But the best way to make a good game on Wednesday is to win on Sunday and have trust in the performance of different players.”
City will be without playmaker David Silva for the trip to Madrid after the Spaniard suffered a hamstring injury in midweek.
Pellegrini said: “He will not be fit for this week. He will need two or three weeks to recover. He will play in the final – that is the target!”
Pellegrini, speaking at his pre-match press conference, delivered a more positive update on midfielder Yaya Toure, who is now back in training. The Ivorian will not play at Southampton, but could be back in contention for Madrid.
“In this moment we don’t know, but he has some options,” said Pellegrini.