The former Arsenal defender believes Rooney is the victim of Louis van Gaal's system as he is being asked to play an unfamiliar role, just as van Persie did before he left for Turkish club Fenerbahce in the summer.
Responding to a question from a United fan on the arrival of Anthony Martial impacting Rooney, Keown wrote in his column for the Daily Mail: "It's an interesting one.
"I can see certain similarities between Wayne's current appearance and that of Robin van Persie last season. It feels like déjà vu.
"Once Sir Alex Ferguson left, Van Persie suffered a dip and last season he looked a far cry from the player he once was. But was he really past his best or was he suffering as a result of the system and instructions from the manager? It could be that the job he was asked to do led to a downturn in performance.
"Now it looks like Rooney is being dampened down in the same way that Van Persie was.
"He has stopped scoring goals and I'm not seeing the same spark in his game. Wayne is always willing to sacrifice himself for the team but there's not the same satisfaction and I wonder how much he is being affected by United's system.
"Martial has scored goals and alleviated some of that pressure but Wayne will want to be scoring goals again, and quickly."