Ferguson left Rooney out of the United line-up for Tuesday's Champions League defeat by Real Madrid, since when it has been suggested the Red Devils boss would be willing to accept an offer for the striker this summer.
However, speaking ahead of Sunday's FA Cup quarter-final with Chelsea, Ferguson denied that was the case.
"He will be here next year, you have my word on that," he said.
"There is no issue between myself and Wayne Rooney. To suggest we don't talk is nonsense.
"He understood the reasons completely. Tactically we got it right. We don't always but we did then.
"There are no issues with the player and he will be involved on Sunday.
"I left out Shinji Kagawa after he scored a hat-trick. I thought I would get more stick for that."
Ferguson is still bitter about the circumstances of Tuesday's defeat, in particular the dismissal of Nani, on which the entire contest turned.
"It is hard to keep your faith when you have things like that," said Ferguson.