Hughes is regarded as one of the best young talents in English football. The likes of Manchester United, Manchester City, Arsenal, Chelsea and Liverpool all had him watched last season - even Barcelona sent scouts to Pride Park to look at the Rams academy product.
Liverpool were heavily linked with a move for the 18-year-old during the summer, but Derby received no formal bids for the player.
The January transfer window is expected to see further interest in Hughes and McClaren accepts it will be difficult for the club to retain his services in the long term.
"Our job is to make sure he makes it, and eventually he will be too good (for Derby)," said McClaren following his first game in charge against Leeds on Saturday, which saw Hughes on the scoresheet in a 3-1 win for the Rams.
"What we need behind that is players coming through to replace him."
Meanwhile, Hughes has withdrawn from the England Under-21 squad for the forthcoming games against San Marino and Lithuania due to a groin injury.