A group of seven Manchester City youngsters are set to be included in the squad for Sunday's tie at Stamford Bridge, with the club to rotate heavily ahead of a Champions League fixture at Dynamo Kiev on Wednesday.
Defenders Tosin Adarabayio and Cameron Humphreys, midfielders Brandon Barker, Manu Garcia and Aleix Garcia as well as strikers David Faupala and Bersant Celina were omitted from the club's under-21 side on Saturday in anticipation of being selected.
Aware of the possibility that his fledgling side could be badly outclassed, Pellegrini urged supporters to understand his reasoning, saying it would be different if circumstances had permitted.
"I think it's not a real game [against Chelsea], of course; not enough to pay the ticket," the Chilean told reporters. "I always give a lot of importance to the cups. They must think why [City are fielding reserves].
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"We always try to play a strong team in the cups, and it would be very nice to finish with a game at Wembley, but there are some moments when you have to prioritise because you don't receive any help and you could damage your prospects.
"The fans want to see a good game but we told them one week ago that we are going to play a young team. If the people want to continue going to the stadium, that's for them."
Pellegrini has expressed his frustration with the scheduling of the fixture in such close proximity to the Champions League and next Sunday's Capital One Cup final, in which his men are due to play Liverpool, on many occasions.
And the 62-year-old took to the chance to reiterate how he felt it was a pity that the FA Cup should be relegated in terms of importance, but stated his hands are tied on the matter.
"I have enough problems trying to manage a team, without managing the FA," he continued. "But the reality is that we must make some changes.
"Maybe [the tournament] without replays can be one solution. Someone said we must eliminate one cup, but I think the cups are good. All the stadiums are at full capacity, even if it is a League Two team.
"So I think fans like the football. I think we should continue with the FA Cup because it is very traditional, but we must make some [better] arrangements."