Chelsea will play Arsenal at the Emirates on 29 October, two days after they face City at home in the Premier League. Arsenal play Crystal Palace a day earlier on 26 October. There are also fourth round games scheduled for the following day, Wednesday, but the Football League have decided that Chelsea must play on the earlier of the two days.
Asked about the timing of the fixture today, Mourinho said: "My thought is that I have to make a decision, and my answer is the under-21 team will have a very good experience in the Capital One Cup. We play Sunday against Manchester City, and Tuesday against Arsenal when the people decide the fixtures.
"The players have ... two days. It's something I have to accept because I have no other option, but I have to prioritise, yes. The league is more important. After that we go to Newcastle, too, and probably it will be a good chance for the kids to play a good match."
Chelsea's Under-21s squad itself has been considerably weakened by the club's policy of loaning out many of its players who are just outside the first team group. Chelsea currently have 26 players out on loan, many of whom would be eligible to play Under-21s football including the likes of Nathaniel Chalobah, Josh McEachran and Lucas Piazon.
The Football League has been put in an impossible position by the schedule. The Arsenal v Chelsea tie, as well as City's Capital Cup tie against Newcastle have both been selected for live broadcast by Sky Sports. As such, one has to be played on Tuesday and one the day later.
In the previous round, City played Wigan in the Capital One Cup two days after beating Manchester United at Old Trafford. It is felt that it would be fair if, this time, City had the extra day's rest.
It has also been noted that Tottenham also played their Capital One Cup tie on Tuesday against Aston Villa two days after their Premier League game against Cardiff City. They too are due an extra day's rest. The Chelsea tie cannot be scheduled on the same say as Spurs play because the Metropolitan police will not permit both north London clubs to play at home on the same evening.
Ahead of tomorrow's Premier League game against Tottenham, Mourinho refused to discuss his opposite number Andre Villas-Boas, who worked with him as an opposition scout at Porto, Chelsea and Inter Milan. The relationship between the two has gradually deteriorated since Villas-boas left Mourinho during his time in charge of Inter to pursue his own coaching career.
Mourinho said: "I'm not keen to discuss relationships with the media. It's a personal thing, and I'm not here to discuss that. I don't care about what he says. I'm not here to comment on what he says. I'm not interested."