The Toffees beat Wigan Athletic to the 18-year-old's signature, and have signed him up on a five-and-a-half-year deal.
"I am very excited to be joining Everton," Stones told the club's official website.
"I've been very impressed with everything I have seen at Finch Farm already. Now the hard work begins."
Stones, a highly-rated young right-back, has caps for England at Under-19 level.
He made his first-team debut for Barnsley in March last year.