Josep Maria Bartomeu came under heavy pressure to step down amid turbulent scenes at the Catalan giants.
A vote of no-confidence motion was taken against Bartomeu, and after a meeting held on Tuesday afternoon, he decided to resign.
It all started with scrutiny, particularly when star player Lionel Messi attempted to quit the club.
It remains to be seen who his successor will be, but it appears there will be a huge shake-up at the Nou Camp as they aim to bounce back from their few months of turmoil.
Bartomeu took charge of Barcelona in 2014 following the resignation of Sandro Rosell, and despite early success under his reign things turned sour recently.
As recently as Monday Bartomeu appeared confident about the future of Barcelona, and insisted they would win another title soon.