Shan takes over the position from Josep Gombau, who has left the club after 18 months in charge.
Monchi, the club's football chief, expressed his excitement about the talent of Aston Villa's Academy players.
He praised Shan's ability to develop young players, citing his successes with the Under-18s, including winning the league and the FA Youth Cup.
The club is now looking forward to Shan's work with the Under-21s, with the goal of helping them grow and improve.