Shwartz will also serve as music director of the San Francisco Symphony Youth Orchestra, replacing SFS resident conductor Edwin Outwater. Outwater will remain resident conductor, leading education and subscription concerts.
Shwartz previously served as assistant conductor of the Delaware Symphony and Pennsylvania's Reading Symphony.
"Benjamin Shwartz is an insightful musician," music director Michael Tilson Thomas said. "He possesses a rare enthusiasm for working with young musicians and for introducing young people to music."