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.