The number of killings last year was 11 percent down from 46 in 2018, the San Francisco Chronicle said.
The number of other violent cases also dropped in 2019, with that of shootings down by 6 percent and overall violent crimes down by 8 percent, according to the local daily.
The last time the number of homicides was as low as last year's count was in 1963, when the city had 100,000 fewer residents, the newspaper said.
City officials attributed the improvement in statistics to joint efforts by law enforcement agencies and community groups, including anti-crime organizations, to divert resources to combat crime.
Official data showed about 71 percent of the murders in the city were resolved last year, much higher than the proportion of 20 percent in the 1990s.
However, despite a 3-percent reduction in car break-ins last year, San Francisco is still troubled by a high number of auto burglaries, which make the city a place with the highest property crime rate across the United States.