The appointment is with immediate effect.
Commenting, BBA chief executive Angela Knight said: "Marcus Agius is taking over as BBA chairman at a time of great change and challenge for the banking industry in the UK. He succeeds Stephen Green who has been a strong supporter of the City and who is moving on to spearhead the government's trade policy.
"The banking industry is facing fresh challenges as it works to play its full part in the UK's financial recovery. Marcus Agius, in his role as Barclays' group chairman, has helped the global universal bank grow and successfully weather the last three year's financial turbulence and brings a sound understanding of the City, the key issues facing the industry and an international perspective which reflects well the BBA's broad global membership.
"I am delighted that Marcus has agreed to become the new chairman of the BBA and we all look forward to working with him."