Silberling was born in Washington, D.C., the son of Joyce Anne (Tucker), a travel consultant, and Robert Murray Silberling, who was Vice President of CBS Entertainment Productions. His father was born Jewish and his mother converted to Judaism. Silberling attended the University of California, Santa Barbara and graduated with a B.A. in 1984. He later studied film directing at the UCLA Film School.

Silberling began his entertainment industry career before completing his studies. In 1986, he became a Production Assistant for a children's program. He then began to direct television and film. Silberling's 2002 film, Moonlight Mile, is loosely based on his bereavement following the murder of his girlfriend, Actress Rebecca Schaeffer, in 1989. In 2006, Silberling's movie 10 Items or Less was the first movie made legally available for download during its theatrical run. This became possible through ClickStar and Silberling's close relationship with its owners Morgan Freeman and Lori McCreary.

Silberling previously dated Rebecca Schaeffer, whom he met at UCLA film school, until the time of her murder in 1989. He is currently married to the Actress Amy Brenneman, whom he met on the set of NYPD Blue and with whom he has two children, Charlotte and Bodhi. In 2000, the couple purchased a home in Chilmark, Massachusetts prior to moving to West Tisbury, Massachusetts in 2011.

Silberling was approached by Warner Bros. as one of the candidates to direct Harry Potter and the Sorcerer's Stone in 1998. Although he began to enthusiastically plan the film in his mind and was ready to sign on to direct it, Chris Columbus was ultimately chosen as the Director.