The goal means he surpasses club legend Charlton as the all-time leading United scorer.
And Charlton was all praise for 31-year-old Rooney.
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I can honestly say that I’m delighted for Wayne
Sir Bobby Charlton
"It’s over 40 years since I scored the last of my 249 goals for Manchester United, so I must admit that I have become used to the honour of being the club’s all-time top goalscorer!" he told United’s official website.
“We have had some incredible strikers here at Old Trafford and they have scored a lot of goals, but it has been fairly obvious for a while now that Wayne Rooney was going to be the one likeliest to break my record, and now that day has come, I would be lying to say that I’m not disappointed to have lost the record.
“However, I can honestly say that I’m delighted for Wayne. He deserves his place in the history books.
Sir Bobby Charlton has congratulated Man Utd's new record goalscorer Wayne Rooney
Rooney scored in the fourth minute of stoppage time at Stoke
“He is a true great for club and country, and it is fitting that he is now the highest goalscorer for both United and England. It has been great to watch him every week since his arrival at Old Trafford in 2004; he set the tone with a wonderful hat-trick on his debut and he has thrilled us all in the years since, going on to enjoy a hugely successful career.
“I was 35 when I retired. Wayne is only 31 and still going strong, so I don’t think he’s done by a long stretch yet.
“He continues to show that he can contribute goals, assists and performances whenever called upon, he will raise the bar even further before he calls it a day. Now he’s the man to beat, and I can’t see anybody doing that for a long, long time."