The Blues' player of the season for successive years has made just one appearance this term and was left out of the side to face Manchester United on Monday.
Speculation over his future intensified with reports that his father, who is also his agent, was spotted at Arsenal but Mourinho says the Spaniard is happy at Stamford Bridge - as he is to have him.
"He didn't play against Man United, it was my option. I have always reasons for the options," said Mourinho, speaking ahead of Friday's European Super Cup clash with Bayern Munich.
"I feel that it's my duty to explain to the players the reasons for my options - and I do.
"I don't feel it's my duty to explain to the media the reason for my options. I don't always do (it).
"Everything is clear between me and the player. We have no problems.
"I think he's a very important player for us. He wants to be a very important player for us.
"He wants to stay. I want him to stay, the club want him to stay. There is no story."