Team owner Jed York on Monday called McCloughan's departure "a mutual parting" and said Trent Baalke, the director of pro personnel, will lead the 49ers through next month's NFL draft.
Last week, NFL.com reported that Baalke would inherit McCloughan's duties, and York described the team's new front-office structure during a conference call with reporters.
York called McCloughan's leaving "a private personnel matter" and wouldn't elaborate, saying "I want to respect Scot's privacy." NFL.com has reported the change was made because of personal issues with McCloughan and not football matters. York said the team waited five days to address the changes because he gave McCloughan his word he wouldn't comment on the matter for that time.
York said he is undecided if he will fill the GM position but said he's totally comfortable with Baalke having final say in the draft room.
"Trent has all the information we need," York said.
York said that per his contract, McCloughan couldn't work for another NFL team until after the draft. York wished McCloughan his best, but when asked about the executive's legacy, said, "You'd have to ask him."