Gill confirmed the talks after announcing that Nemanja Vidic had agreed a new long-term contract with the club.
Rooney still has two years left to run on his current contract with United.
Gill said: “The current intention is to meet with Wayne and his advisors when we’re back from tour and he’s back from holiday with a view to sorting out a new deal for him.
“It’s clear from what he has said and what the club have said that both parties are very keen to sort things out and secure his long-term future at United.
“Given his desires and what he means to the club we’re very confident that can be achieved.”
