Dushku currently resides in Laurel Canyon, Los Angeles, California.
She has stated that she dated Major League Baseball player Brad Penny.
In late 2008, Dushku broke up with Family Guy creator Seth MacFarlane; she is currently dating Los Angeles party promoter and DJ Brent Bolthouse.
Dushku is the CEO of her production company Boston Diva and serves as a producer on her yet-to-be-released Fox sci-fi series, Dollhouse. She is an avid fan of the Boston Red Sox.
Throughout her career, Dushku had refused to appear in nude scenes, saying that people have "a better chance of seeing God than seeing me naked."