Rooney was dropped to the bench for Tuesday's Champions League match against Real Madrid, United's biggest game of the season, sparking suggestions he could be headed for the Old Trafford exit.
Ferguson on Friday denied that United would look to sell Rooney at the end of the season.
Now the manager says United will offer the 27-year-old Rooney a new deal before the current one expires at the end of the 2014-15 season.
Ferguson says "there's no issue with his contract. When it has to be renegotiated it will be. We don't want players to leave."