The 18-year-old, who had two years remaining on his contract with the Dutch second division outfit, is expected to represent Everton's Under-23 side next season with the view to progressing into the first team.
"It feels great to be an Everton player. It's a nice opportunity for me and I love it here already," Markelo told Everton's official website.
"I heard something about two weeks ago after a tournament I played in and I was very happy. I decided immediately that I wanted to come to Everton.
"I'm looking forward to the season now. I have three years here and I hope to get plenty of playing time, develop as a player and then just keep making steps forward towards the first team."
Markelo, who made 30 appearances at Under-19 level last season, is a Netherlands Under-18 international.