A Gap Inc. spokesperson said it will close to the public on July 1, and its lease will expire on July 31.
The company said it is looking at other locations in downtown San Francisco that "will better serve the needs of the business and our customers."
Gap Inc. also said it has opened four new stores (Old Navy, Gap, Banana Republic and Athleta) at the company's newly remodeled global hub at 2 Folsom St. in San Francisco last year.
MORE: Nordstrom to close both Downtown San Francisco stores, company confirms
The Old Navy on Market St. opened in 1997.
VIDEO: San Francisco stores that are now gone
San Francisco stores that are now gone
Old Navy has other stores around in the Bay Area in San Francisco, Daly City, Colma and Emeryville.
The Market St. closure comes after Nordstrom and Banana Republic have decided to close its stores in the Union Square and Market St. area.