The United and England legend backed up Sir Alex Ferguson's claims that Rooney would still be at Old Trafford next season.
Reports have emerged that Rooney is a target for Bundesliga giants Bayern Munich in the summer, but Charlton insisted Ferguson would not let the 27-year-old go.
"I think that is a bit premature," said Charlton when told of the alleged interest from Bayern. "I don't know everything that happens at Manchester United, but I know a little.
"Wayne Rooney maybe has had an injury and has not performed as well as he might have done, but that doesn't mean to say that you get rid of him.
"Sir Alex Ferguson came out and said that he had no intention of letting Wayne Rooney go anywhere.
"You have to abide by that and I believe it, 100%. He is a great player - why should we get rid of a great player?"
Charlton was speaking in Rio de Janeiro ahead of Monday's Laureus World Sports Awards, where Bayern's honorary president Franz Beckenbauer admitted he would love to have Rooney at the club.
He said: "I would be very, very happy if Wayne Rooney decided to come to Bayern Munich, but is this a rumour or is it true? I don't know!"