The package was discovered shortly after 1:30 p.m. in the 2000 block of 15th Street, Officer Albie Esparza said.
A bomb squad was called in and streets were closed.
Esparza said at 4 p.m. that the situation had been cleared and that streets have reopened.
The incident disrupted service on San Francisco Municipal Railway's F-Market line, Muni officials said.