The 16-year-old Cooper, who is from Christchurch, New Zealand, took his first start in a UCI World Cup and then blitzed the field to beat favourite Jans Schuermans (Belgium) by one minute and 43 seconds in Nove Mesto Na Morave.
Schuermans,19, who won the European Championship last weekend, led on the first lap with Cooper following before the Belgium fell back and the young kiwi took control. He won comfortably from Schuermans with Spain's Pabli Rodriguez third.
The Christchurch Boys High School student won a warm-up event in Switzerland last week and was using the World Cup to prepare for the upcoming world championships in Champery, Switzerland, at the end of the month.
His European success continues a stunning season for the young Cantabrian who won the Oceania and New Zealand under 19 titles. He also became the youngest rider to win the famed Karapoti race and set a new record when he won the Motutapu mountain bike race.
"This was the first time I rode a World Cup. It was hard. Jens went very quickly in the first lap, but I could stay with him and eventually win the race," said Cooper.
See more coverage of the UCI Mountain Bike World Cup in Czech.