The clothing retailer said it is searching for a replacement.
Gap North America president Marka Hansen said: 'On behalf of everyone at Gap brand, I want to thank Charlotte for all her efforts. We wish her the best in the future.'
In addition, GapBody division president Tom Wyatt has been named president of Gap Outlet with immediate effect.
Wyatt succeeds Diane Neal, who left the company in November, and will continue to report to Hansen.
Hansen said: 'Tom has led a number of well-respected companies with large brand portfolios during his 30-year career in retail. We're confident that he'll continue to build on the foundation for growth that he has established with GapBody, while he works with the Outlet team to identify opportunities to drive their business forward.'
Wyatt joined Gap a year ago from Cutter & Buck, where he was president and chief executive. Prior to that, he was chairman and chief executive of Parisian, a chain of speciality department stores owned by Saks.
Gap has announced several major management changes in recent months. Last week, former Gap North America president Cynthia Harriss left the company. Gap chief executive officer Paul Pressler - who has headed the US retailer since 2002 - resigned last month, after more than two years of sliding sales at the group.
Gap revealed net sales down 4 per cent to US$2.34 billion (£1.18 billion) for the five weeks to December 30.
The company's comparable store sales decreased 8 per cent, with Gap North America down 9 per cent, Banana Republic up 2 per cent, Old Navy North America decreasing 10 per cent and International sliding 8 per cent.
The company said that it expects the percentage increase in sales per sq ft to be in low single digits by the end of the fourth quarter of the current financial year.