Fabregas, who left Barcelona’s academy to join Arsenal in 2003, has long been linked with a move to the Spanish side.
Arsenal manager Arsene Wenger told his club’s official website: “We have been clear that we didn’t want Cesc to leave and that remains the case.
“However, we understand Cesc’s desire to move to his home town club and have now accepted an offer from Barcelona.
“We thank Cesc for his contribution at Arsenal and wish him future success.”
Barcelona have confirmed that Fabregas will undergo a medical on Monday before signing a deal with the club.