The 34-year-old Wales captain, who spent last season on loan at second-tier Stoke, made 73 appearances during his three-year spell at Goodison Park.
"Everton can confirm Ashley Williams will leave the club when his current contract expires at the end of the month," the Merseyside outfit said on their official website.
Fellow central defender Phil Jagielka revealed earlier this week he was also leaving after 12 years with the Toffees.
Everton also announced that Luis Boa Morte has been appointed assistant manager.
The former Arsenal, Fulham and West Ham player, 41, has teamed up again with Everton boss Marco Silva after a spell together at Sporting Lisbon.