The death was reported at about 4:30 a.m. at a home in the 2100 block of Quesada Avenue and was originally reported as a possible suicide, San Francisco police Officer Albie Esparza said.
Officers found the boy, identified by the medical examiner's office as 16-year-old Andy Zeng, dead inside the home.
Zeng was a San Francisco resident, but did not live at the home where he was found, police said.
The medical examiner's office has ruled that Zeng's death is suspicious, so further investigation is needed to find out how he died, Esparza said.
No other details about the case were immediately available, he said.
Anyone with information about the death is asked to call the Police Department's anonymous tip line at (415) 575-4444 or send a tip by text message to TIP411.