Hughes has signed a deal at Pride Park until 2016, and Clough is delighted to secure the 18-year-old's immediate future after he was linked with several top Premier League clubs.
The 47-year-old told BBC Radio Derby: "He's had a fantastic season and learnt so much over the last 12 months.
"There is a pay rise which he thoroughly deserves and the extra year. I hope there will be a new one within the next 12 months."
The England Under-21 international has made 32 appearances in the Championship this season.