Shan is promoted from the U18s as Josep Gombau leaves Villa and the U21 post.
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Villa football chief Monchi explained: “The Club is very excited by the talent of our Academy players.
"Jimmy has shown his ability to conduct and develop players with the Under-18s winning the league and the FA Youth Cup and we look forward to watching him work with our Under-21s.”
Gombau leaves after 18 months in charge of the U21s, the Spaniard led Villa to the round of 16 in the UEFA Youth League last season.