The 35-year-old has struggled with injury in recent years and has made just six appearances in all competitions this term, with Javier Mascherano and Marc Bartra preferred alongside Gerard Pique at center 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 news 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, teammates, managers, media - thank you everyone for everything you've done for me."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.