Mee Mee Bakery and Walgreens on Stockton Street near Vallejo Street were forced to close temporarily.
When the public health inspector initially checked on the buildings, they were labeled as imminent health risks to the public.
After serious cleaning and sanitizing, both were allowed to reopen around 3 p.m.
During a routine visit Thursday, a health inspector found mice in the bakery. The bakery is a popular tourist destination where fortune cookies can be made to order.
On Friday vermin were discovered at the Walgreens next door. It closed for cleanup.
"You can smell the rat infestation in there and I've mentioned it to management before at Walgreens and nothings ever done," said customer Jeffrey Bilbrey.
"Every store is so closely populated, okay, there's no way you can clean up the rats or the cockroaches. You know you clean one place, they go to next store then they come back again eventually," Bilbrey said.
The San Francisco Department of Public Health insists the infestation is limited to mice.
No matter what kind of rodent it is Kam Hui now refuses to eat in Chinatown.
"I used to eat a lot in Chinatown, but I stay away from the restaurant business," he said.
"I'm sure the mice are not in my bag of fortune cookies, nor the mice droppings," said Mee Mee Bakery customer Edward Weiner.
The stores had to clean, sanitize and remove all mouse droppings.
The spokesperson did not say if this vermin outbreak is linked to the central subway system dig going on nearby, but the San Francisco Chronicle reported last week the dig is connected to a rat outbreak near Washington Square Park, only a few blocks from these stores.