Visa Inc. said Chief Executive Officer Charles Scharf is resigning his post after advising the board that he can no longer spend enough time in San Francisco "to do the job effectively."

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The San Francisco-based payments network said Mr. Scharf will be replaced by Alfred Kelly, 58, a member of Visa's board and a former president at American Express Co. In an interview, Mr. Scharf said his departure is connected to a need to be closer to his family in New York.

"I think to do this job properly you need to be committed to spending the appropriate amount of time in San Francisco. Given my personal situation, I don't feel that I can do that right now," he said.

In a memo to Visa employees Monday, Mr. Scharf noted that his daughters, parents and extended family are all on the East Coast. Before taking the Visa job, Mr. Scharf lived in New York.

"I love working and running this great global company and I am sad to have reached the conclusion that I should step down, but running a San Francisco based company just doesn't work for me personally right now and wouldn't be fair to Visa," Mr. Scharf said in a news release. Mr. Scharf also will step down from Visa's board of directors.

Mr. Scharf, 51 years old, took the helm of Visa in November 2012 after spending most of his career in the banking industry, including a seven-year stint running the enormous retail-banking division of J.P. Morgan Chase & Co. During Mr. Scharf's tenure, Visa's stock generated a total return including dividends of 144% versus 64% for the S&P 500.

The payments industry has expanded aggressively into digital channels during Mr. Scharf's time at Visa. He also has had to navigate an often-tense relationship with some of the nation's largest merchants, including Wal-Mart Stores Inc.

Last year, Visa bought its European counterpart Visa Europe for more than $20 billion in a long-awaited deal that brought the payment network's global operations under one roof.

In an interview, Mr. Kelly said he feels well-prepared to take on the Visa job even though he has technically been out of the industry for some time. Earlier this year, Mr. Kelly was named CEO of Intersection, a technology and media company behind an initiative to bring public Wi-Fi to New York City.

"My [Visa] board service has allowed me to stay enormously close to an industry that I stayed almost 2 1/2 decades in prior to this," Mr. Kelly said. Since leaving AmEx he also served as the CEO of the 2014 NY/NJ Super Bowl Host Committee and as chairman of the 2015 Papal visit to New York City.

Visa processes credit-card and debit-card payments on behalf of the nation's banks and merchants. It doesn't set interest rates or issue cards. The company has a market value of $190 billion, more than one-third larger than rival MasterCard Inc.

Robert W. Matschullat, Visa's independent chairman, described Mr. Scharf in a statement as a "visionary CEO, highly successful by any set of metrics."

Mr. Kelly will join the company on Oct. 31 as CEO-designate. Mr. Scharf will serve as an adviser to Mr. Kelly starting on Dec. 1 for several months.

"We are thrilled to have found someone with Al's expertise and knowledge to take Visa to even greater heights," Mr. Matschullat said in the statement.

Mr. Scharf said he approached the board in mid-September to advise them that he was considering stepping down, and then submitted his resignation on Monday morning.

Visa was scheduled to hold a conference call with Wall Street analysts and investors later on Monday. The company is slated to report quarterly earnings on Oct. 24.