The 35-year-old has decided to call time on his career at Camp Nou, 15 years after making his debut for the club
The 35-year-old has struggled with injury in recent years and has made just 12 appearances in all competitions this term, with Javier Mascherano and Marc Bartra preferred alongside Gerard Pique at centre-back.
His current deal runs until 2016 but Puyol has revealed that an agreement has been reached with the club to erase the final two years of his contract.
"The club knows of my decision. It doesn't mean that I am leaving today, there are three months of the season left to play," he told reporters at a press conference on Tuesday.
“I do not know what I will do after June 30. I will need to rest and think. We will see then.
"I wanted to call this press conference to thank everyone, directors, team-mates, managers, media - thank you everyone for everything you've done for me."
Puyol admitted that his recent physical problems did have a key impact in his choice to quit.
"After the two aggressive surgeries, it's taking me a lot to get back to the level I demand myself to keep playing. More than I thought and much more than what doctors told me. That's why I made this decision," he said.
The defender came through the youth ranks at Camp Nou and made his debut for the club in 1999, before going on to rack up nearly 600 appearances for Barcelona in all competitions.
Puyol becomes the latest experienced head to announce his departure from the reigning Liga champions after Victor Valdes revealed last season that he will leave when his contract expires this summer.