The news, which the London-based financial institution said was "in mutual agreement" with the board, means that Flint will not be carrying out his daily duties after Sunday, but that he remains available to assist with the transition.
"On behalf of the Board, I would like to thank John for his personal commitment, dedication and the significant contribution that he has made over his long career at the Bank. Today's positive interim results particularly reflect John's achievements as Group Chief Executive," said Mark Tucker, group chairman of HSBC, in a statement.
He said that HSBC is still in a strong position to "deliver on its strategy."
Flint said in a statement that it was a "privilege" to spend his entire career with HSBC, "rising from International Officer Trainee to serve as Group Chief Executive."
"I am grateful to my wonderful colleagues at the Bank for their support during my career, and I am proud of what we achieved together," Flint said.
He had spent almost 30 years with the bank.
"I will be sad to leave but I do so looking forward to a new personal challenge, and confident that our people will continue to serve the Bank's stakeholders in the best possible way."
The bank's board said it has begun looking for a new group chief executive, and will be considering candidates inside and outside of the firm.
Noel Quinn, in the meantime, will be interim group chief executive.
Quinn is currently chief executive of global commercial banking at HSBC.
HSBC is one of the world's largest banking and financial services organizations, with more than 40 million customers and a presence in 65 countries and territories, according to the bank.