Bansal would, however, be an advisor to the company, Flipkart said in a statement.
In a development that comes weeks after the rejig at the top level, the company also said that Ankit Nagori, Chief Business Officer, Flipkart, is also moving on to start an entrepreneurial venture in the sports domain.
"Mukesh Bansal, Head of Commerce Platform, Flipkart is moving out of his active role to be an advisor to the company," it added.
"Ankit has played an instrumental role in introducing newer initiatives at Flipkart and building the marketplace model for the company. Sachin and Binny will be supporting Ankit in his new initiative and will be his first investors," the statement said.
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Thanking Mukesh and Ankit for their "invaluable contribution" to the growth of Flipkart, the company has wished them "all the best."
In a top management rejig, Flipkart last month had appointed Binny Bansal as the Chief Executive Officer and Sachin Bansal as the Executive Chairman.
Mukesh, in a letter to employees, said, "My incredible journey with Myntra and Flipkart comes to an end. It has been amazing nine years filled with lot of learning, privilege to work with outstanding people and chance to participate in building future industry of India that will impact hundred of millions of people."
Mukesh also expressed confidence that the leadership team at Myntra, lead by CEO Ananth Narayanan, will make it an "iconic company" which will change the face of fashion industry in India.
Talking about leadership team at Flipkart, Mukesh said, "With the calibre of this team, I am very confident that Flipkart is in safe hands and this team is eminently capable of charting the course for next phase of Flipkart journey."
He added: "I am very excited with Binny coming in as CEO and my transition will enable him to work directly with CPleadership... Binny, along with the leadership and the amazing talent pool at Flipkart will do justice to any mandateand continue to push the boundaries for e-commerce /Internetbusinesses in India and beyond."
"I am looking forward to a long break after mytransition and catching up on my reading, travel and fitness. I will be spending bunch of time with my kids and catch up onall the fun I have missed with them all these years," he added.