Steven Burky was arrested in Santa Monica on Monday at the nursery school where Violet Affleck, one of Garner's two daughters with husband Ben Affleck, is enrolled.
Los Angeles County District Attorney's spokeswoman Jane Robison says Burky will be arraigned on Thursday.
Garner was granted a restraining order against Burky in November 2008 after she told the court she believed he posed a threat to her and her family. Garner alleged that Burky had been stalking her since 2002.
The former star of the television series "Alias," Garner has also appeared in films such as "Juno" and "The Kingdom."