The Cannondale Factory Team rider, who turned 19 in New Zealand on Sunday, took out the World Cup at Mont-Sainte-Anne to celebrate a remarkable return after recovering from a debilitating virus that forced him out of competition since May.
With the North Canterbury teenager still 18 years of age in North America on Saturday, team officials informed that his win is the youngest by any cross country rider in a UCI Under 23 World Cup.
"It is huge really. It's a huge confidence boost to come back from a rough couple of months out with illness. It really means a lot to me and I really want to thank everyone for sticking by me through thick and thin. It's good to be back on track," Cooper said.
The young star became ill at the time of his under 23 World Cup debut in Germany in May, finishing down the field. He remained at his base in Germany for the next month but after he did not respond to treatment, he returned to his home in Woodend near Christchurch.
Slowly his health improved and last month he got back on the bike, returning to race in Andorra two weeks ago where he placed 18th.
"I only had two and a half weeks back in full training leading up to Andorra, and I had a rough week leading in. But I knew that a couple more weeks of training under my belt and with my health 100 per cent then I was going to be on for a good race," he said.
"This whole week, my legs have been great, and I have been enjoying riding the course. I woke up this morning feeling good and I felt that something special might happen but I didn't want to believe it until I crossed the line."
Cooper was fourth after the opening lap before pushing through to the lead with two others, dropping Swiss rider Reto Indergand on the fourth of six laps and then Germany's Julian Schelb on the next lap.
"I wanted to play it by ear and see how I went. I felt great on the first lap but I was unsure how I would feel on the fifth and sixth laps and that's where it really counts.
"With a lap and a half to go I got a wee gap. I was not planning to escape that early but after I opened the gap I decided to drill it from there, and I buried my head and went for it.
"I can't tell you how much it means. It's really tough to find yourself in the position of being really ill. I know it's something every athlete faces at some stage in their career, but it was a new position for me. To get a result like this means so much after all this hard work to get back in shape."
Cooper won in 1:17:53 to be a minute clear of Schelb with Indergand 1:41 back.
He will celebrate his 19th birthday with his team before returning to Germany to begin final preparations for the UCI Mountain Bike World Championships starting in Pietermaritzburg, South Africa starting in two weeks.