United’s leading goalscorer has struggled to get game time under Jose Mourinho this season.
Rooney, 31, started just 15 Premier League games as the Red Devils finished in sixth place.
The England international is not expected to start in the Europa League final on Wednesday, when United face Ajax in Stockholm.
Rooney has been linked with an Old Trafford exit this summer, with Everton and clubs in China said to be keen on the attacker.
“You hope (he doesn’t leave) but the way the season’s gone, particularly since Christmas, he’s not been involved as much as he’d probably have liked,” Neville told Sky Sports.
“He wants to play in the biggest games and when it comes to Wednesday night I’d be surprised to see him in that starting XI.
“It looks like he’s on his way out of Manchester United and it happens towards the end of your time.
“You get the signs that now is the time to leave, and probably now is the time.
Mourinho is expected to have a busy transfer window this summer, especially if Champions League football returns to Old Trafford next season.
Antoine Griezmann, Kylian Mbappe and Gareth Bale have all been linked with United to solve their goalscoring woes.