During his tenure, he instigated the agency's rebranding from its previous name, Everest Advertising.
His exit follows the recent departure of Mahesh Chauhan, the agency's former president, who left last month to become the president of its sister agency, Rediffusion DY&R.
Banerjee said he was leaving the agency to move on to bigger challenges. "The charm of building Everest as a brand was good, but it's stable now and doing quite well for itself."
Banerjee began his career at Contract in 1988. Two years later, he joined Clarion. In 1998, he joined Leo Burnett, before moving to Everest in 2004.