The Portuguese made it clear he did not want Rashford to be participating in the upcoming European Under-21 Championship in Poland.
England boss Gareth Southgate has now selected Rashford for the senior squad, which means he will miss out on U21 duty, but the 46-year-old claims that the decision was not made just to appease Mourinho.
Southgate said: "No, I didn't speak to him about it. I just let him know where I was heading at the end. I am not in a position where I can make decisions to keep people happy. I'm not going to achieve that.
"If I am trying to keep Jose happy, then that's going to be fairly difficult. So I have got to make decisions that are right for England seniors, long term. I'm always mindful of what is right for the players. None of the managers are likely to be around in 10 years, but people like Marcus Rashford will be.
"His relationship with England is key. So we want a good working relationship with the clubs, of course we do. But they have got their own objectives, and they have to make decisions that are right for them. I have to make decisions that are right for England."