The package was reported shortly after 12:30 p.m. near the intersection of Irving Street and Arguello Boulevard, police spokesman Officer Gordon Shyy said.
People in nearby homes and businesses have been told to shelter in place, and surrounding streets have been shut down, Shyy said.
The incident has disrupted service on San Francisco Municipal Railway's N-Judah line, which is switching back outbound trains at Carl Street and Hillway Avenue. Inbound trains are being turned around at Judah Street and 19th Avenue, Muni spokeswoman Kristen Hollandk said.
Bus shuttles are supplementing service in the affected area, Holland said.
At about 1 p.m., two police cars were blocking off the intersection of Irving and Second streets, and an area at the base of the UCSF Medical Center parking garage was cordoned off.