Felix saw off the competition of Borussia Dortmund’s English winger Jadon Sancho and Bayer Leverkusen’s Kai Havertz, who finished in second and third places respectively.
Felix had a blistering start to his debut as a professional at Portuguese side Benfica last season, scoring 18 goals and assisting 10 more in all competitions.
The 20-year-old became the fourth most expensive signing in football history when he completed a £116m move from Benfica to the Rojiblancos in the off-season.
Felix takes over from Juventus defender Matthijs de Ligt, who won the award last year while at Ajax Amsterdam.
He is the first Atletico Madrid player since Sergio Aguero in 2007 to win the Golden Boy award.
“Thanks to Tuttosport for the Golden Boy Award 2019, I am very proud,” Felix said.
“It is the second time that a player from Atletico Madrid has won this award and I am happy.
“Thanks also to Benfica, in particular to coach Bruno Lage, for all he has done for me and my family.”
Previous winners of the Golden Boy award include Lionel Messi, Kylian Mbappe, Raheem Sterling and Mario Balotelli.
Felix impressed for Atletico Madrid in pre-season but is yet to set La Liga alight.
He has two goals and one assist from 13 appearances in all competitions this season, having recently returned to action after a month on the sidelines.