Rooney has recovered from a three-month long undisclosed injury.
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He struck, along with JJ Gabriel as United won 6-0 against Brum. Also on the scoresheet were Jacob Watson, Rafe McCormack, Jay McEvoy and James Bailey as United reached the quarterfinals.
Gabriel, 15, scored the winner in the FA Youth Cup against Peterborough at Old Trafford a fortnight ago.
Making their debuts for United were new signing Charlie Hardy, with the goalkeeping joining from Derby this month and defender Harley Emsden-James, who joined in the summer from Southampton.
