The San Francisco-based company said John Hans Morris will step down as president, but remain with Visa in a different capacity until year end.
Visa said it will also consolidate oversight of its sales, client service, marketing, product development and innovation functions under Chief Operating Officer John Partridge.
Morris joined Visa in 2007, when he was 48, and according to the company played a central role in its March 2008 initial public offering, when it raised about $19.7 billion.
Before joining Visa, Morris had worked at Citigroup Inc
Visa said the management changes will heighten organizational effectiveness and increase the pace of Visa's global alignment.
The company did not give a reason for Morris' departure. Visa spokesman Paul Cohen declined to elaborate, citing a quiet period ahead of the company's expected reporting of fiscal third-quarter results on Wednesday.
Chief Executive Joseph Saunders also said Visa continues, to meet or exceed all our current financial guidance.
Analysts on average expect quarterly profit of 65 cents per share on revenue of $1.64 billion, Reuters Estimates said.
Visa's main rival is MasterCard Inc
Visa shares rose 25 cents to $68.44 in after-hours trading. They had risen 90 cents to $68.19 in regular trading on the New York Stock Exchange.
(Reporting by Jonathan Stempel; editing by Carol Bishopric and Andre Grenon)