Rooney would make his debut as a 16 year-old under David Moyes and famously score a wonder goal against Arsenal, beating David Seaman no less, as Everton defeated the Gunners thanks to his 90th minute winner in October 2002.
At the time, Rooney was still an £80-a-week apprentice, but the goal ended Arsenal's 30 game unbeaten league run and announced the teen to a global audience.
Looking back, Hughes could sympathise with the likes of Seaman, who was left shocked by the talent of Rooney at the time. The defender, who would taste first team football with his hometown club and also captain their U23s, admits facing Rooney daily in training had him reconsidering football as a career.
"In my younger younger days, I was like 9 or 10," Hughes told Tribalfootball.com. "And we had these games at Savio (Salesian College), we didn't really have anywhere to play. And we used to have these showers, we'd all be in the same showers.
"I remember playing the year above myself so he (Rooney) was playing at the time. And I was this 9 or 10 year old and he was 11, and I remember I walked into the shower and he had a hairy chest, hairy b***s, hairy pits, and I remember thinking oh my God who is this lad?!
"We used to train against them quite a bit and I was miles behind. And I was thinking if I'm going to be a footballer as a defender and he is the type of striker I'll be playing every week, I might as well pack it in now because I couldn't get near him."
Hughes says such an early impact was always in the cards for Rooney, who would be sold by Moyes two years later to Manchester United.
He recalled: "He was bigger than you, stronger than you, more powerful than you. You think you'd give him a yard and he'd shoot from 30 yards and put it in the top corner. He could do absolutely everything.
"A year is quite a lot when you're younger, and I remember when he was 12 or 13 he was playing U19s. We used to watch him score hat-tricks, he was playing five years ahead of himself and was the best player on the pitch. I remember when he broke into the first-team, we used to get tickets to go watch, and he was the best player at Everton at 16.
"I used to love the fact that he used to play as if he was playing with his mates in the streets or playing with his mates all the time, even when he made that step to the Premier League, he played with no fear."