The 29-year-old defender joined the Clarets on loan from City in the summer of 2011 and made a permanent move at the start of 2012.
He became only the second player to do so for the club, after Ashley Barnes, and was given a Milestone award from the Premier League, in association with Cadbury.
"When I moved here, if you had said I would be playing 100 games in the Premier League I would have taken that all day long, and hopefully there are many more to come in the next few years," Mee told Burnley’s official website.
Mee was a key part of Burnley’s seventh-place finish last season and is keen to repeat that level of achievement.
"I have been part of the success this club has been having and to play a bit of a part in that has been fantastic," he said.
"It's an important period in this club's history, I guess. It's nice to be involved and I want to be involved in it a bit more."