The 31-year-old joined Manchester City from Everton in August 2016 and went on to develop into one of the Premier League's top defenders - making 293 appearances in all competitions.
Stones also earned 87 England caps, playing a key role at both World Cups and European Championships.
"It's been a rollercoaster, in many ways," Stones said in a tearful video on his Instagram.
"I came as a kid, and now I'm leaving as a man, becoming a father and husband, and on the pitch a very fulfilled player.
"I've lived all my dreams out and lifted all the things I came to achieve. At the start of my career here, I never thought I'd be able to achieve everything.
"Every dream has been smashed out of the park. The fans mean everything to me... I hope I've made them proud.
Injuries have affected his final couple of years at the Etihad Stadium, but the Englishman departs with an impressive haul of six Premier League titles, one Champions League, one Super Cup, five EFL Cups, two FA Cups and one Club World Cup.
That trophy cabinet could still grow in the final two months of his contract, with City in the FA Cup final and second in the Premier League with five games remaining.
A report from The Athletic has stated that interest is expected from leading clubs across Europe.