The 31-year-old is no longer a regular at Old Trafford, slipping down the pecking order this season and being used just 14 times from the off in the Premier League.
Rooney turned down a move to the Chinese Super League at the turn of the year but, with offers still thought to be on the table from the Far East, the England international may be tempted to bring his 13-year spell with United to an end in the coming months.
Mourinho acknowledges the predicament Rooney faces, having also worked with Chelsea legends Frank Lampard and Didier Drogba in their latter years, saying that there is no easy way to deal with the situation.
"It's very difficult because during my career I had this kind of situation of getting players – amazing players with amazing history – in the last period of their career," he told Omnisport.
"When you get players in the last part of their careers, the players with the big history in the club – and I had that everywhere, I had that in Inter, I had that at Real Madrid, I had that at Chelsea.
"Frank Lampard, Didier Drogba, to have them – and in my case I had them in the best period of their career – and then when I returned the second time, I had them in their last period of their career. How difficult it is."
Rooney became United's all-time record goalscorer earlier this year when finding the net for the 250th time, surpassing Sir Bobby Charlton's long-standing record.