The Apple store will move from its current location at 1 Stockton St. to 300 Post St. on the northeast corner of Union Square, city officials said.
The new store will employ about 50 more employees than the current one and will be about 45 percent larger, according to the proposal submitted to the city's Planning Department.
"I can think of no better location for the world's most stunning Apple Store than right here in Union Square," Mayor Ed Lee said in a statement. "I want to thank Apple for their investment in this city and continued commitment to growing jobs in San Francisco."
The site is currently occupied by a Levi Strauss and Co. store that is moving to a new location later this year, according to the city.
Apple also has two other retail stores in San Francisco, on Chestnut Street in the Marina District and at the Stonestown Galleria Mall.
