Baudoin Prot, 63, who has headed the bank since 2011, was stepping down as of December 1 "for personal reasons," the bank said in a statement following a meeting of the board late on Friday.
Prot will be replaced by Jean Lemierre, 64, one of his close advisors and a key figure in negotiating BNP Paribas's settlement with US authorities.
Prot's resignation, which was first reported by a source close to the matter on Tuesday, comes almost three months after the giant French bank pleaded guilty to US criminal charges of violating sanctions on Iran, Sudan and other countries.
Prior to becoming chairman, Prot served as chief executive of BNP Paribas from 2003-2011, the period in which many of the violations of US sanctions law took place.
US officials said BNP Paribas deliberately hid thousands of transactions with Iran, Sudan, Myanmar and Cuba, countries that were sanctioned for terrorism and human rights violations.
The bank agreed to plead guilty to one count of conspiring to violate sanctions, making it the first bank found guilty in a sanctions case.
Prot was not personally questioned by US authorities during the probe, but the difficulty of the settlement negotiations took its toll on the chairman, according to people familiar with the bank.