The club later confirmed Rooney has a knee injury and had been at their Finch Farm training base for treatment on Friday morning before leaving around midday as the rest of the squad headed out for training.
Earlier on Friday, boss Sam Allardyce said he was looking forward to speaking with Rooney and insisted that the former England captain had not asked to leave the club.
Sky Sports News understands the 32-year-old has agreed in principle to make a £12m move to Major League Soccer with DC United.
“My understanding is there seems to have been some negotiation somewhere along the line but as for clarity as to whether Wayne is staying or going we’ll see later on,” said Allardyce.
“I’m comfortable with any player who wants to leave but let’s put this right. Wayne Rooney has not asked to leave and neither has Wayne Rooney had a confrontation with me.”
Allardyce was overseeing one of Everton’s final training sessions before their last Premier League game of the season, which comes at the London Stadium against West Ham on Sunday.