Rooney, 31, made his return to Everton earlier this month, ending a trophy-laden 13-season stay at Old Trafford.
United and England's all-time leading goalscorer, Rooney made just 15 Premier League starts in 2016-17.
But Mourinho is already missing the forward and said he would be tough to replace.
"I miss him a lot, I miss the guy a lot, I think he's a fantastic guy," the Portuguese tactician said, via The Telegraph .
"I'm not the kind of guy that gets normally emotional in my job and I did it with him when he left, but I am sure that he's going to be very good for Everton, and Everton is going to be very good for him.
"Wayne was a very positive influence. We cannot say we are going to improve the group because Wayne left. No way, or the other way around.
"He was such an important guy and a good guy for us. I just think it is a new period without that face, without that leader, without that good influence on us."
Rooney signed a two-year deal at Everton, the club he left to join United in 2004.
While Mourinho wanted to keep the England international, he said Rooney deserved the respect of being allowed to decide his future.
"It was not difficult because he deserves that it's not difficult," Mourinho said.
"He deserves what he got and what he got was our desire for him to stay and our respect by letting it be completely clear that we would like him to stay.
"And at the same time the respect that allows him to be happy, allow him to try to play every game, every minute, which honestly I think he needs.
"At his age I think with his genetic, with his body he's not the kind of – I think with his personality too, I don't think he's the kind of player to be less motivated, not so happy because he's not playing every minute."