The Clarets legend has left his role as Burnley Under-23s boss to take over at Cheltenham Town.
"He's been massive. Having someone who has been a player at the club and involved in the club for such a long time, knowing how the gaffer works, has been massive for the lads," Pepper said.
"For him to come in to the academy after his career has been huge for the staff as well.
"I'm new to the club and he's really educated some of the staff in what it means to represent Burnley Football Club, the culture, the expectations and the values. He's really helped to implement that.
"That vision now transcends further down in to the Academy. I have to really thank him for that because he's really educated me.
"He's been great with the lads, he's very humble, you'd never think that he'd played in the Premier League. I think the lads and the staff have really learned from him and we wish him all the best."