Everton did not disclose the transfer fee, but British media reported the deal was worth around 16.5 million pounds, plus add-ons.
Hackney becomes manager David Moyes' first signing of the summer after impressing for Middlesbrough in the 2025/26 campaign.
"The manager's track record of bringing players from the Championship to the Premier League was a massive part of my decision as well," Hackney said in a club statement.
"Hopefully I can be the next one to do it successfully for Everton."
Hackney, 24, was named the Championship Player of the Season after captaining Middlesbrough and making 41 appearances in all competitions.
Middlesbrough narrowly missed out on promotion to the Premier League, losing to Hull City in the Championship playoff final at Wembley in May.