The 27-year-old moved to Old Trafford from Southampton in a deal worth around £25million in July 2015 but has struggled to make an impact since Mourinho's arrival last summer.
West Brom were hoping to sign Schneiderlin but the France international looks set join former Saints boss Ronald Koeman at Goodison Park after an initial £22million deal was agreed upon.
Mourinho said after United's 2-0 EFL Cup semi-final first leg win against Hull that Schneiderlin was "more than probably going to go to Everton" after a pre-match update from executive vice-chairman Ed Woodward.
"Before the match Mr Woodward told me 'almost there', so I have 'almost there'," Mourinho said. "So I'm sad, I'm happy. I'm sad because I like him and he could be an option for us in a long season.
"I'm happy because this is what he wants - he wants to play every game, to be an important player in the team. So if this is what he wants, I am happy for a very good professional, somebody I can only say good things about."