Bodhi Pine Elfman was born in Los Angeles, California, and raised in Hollywood, Los Angeles. He is the son of actor/director Richard Elfman and Rhonda Joy Saboff, grandson of author Blossom Elfman, and nephew of composer Danny Elfman. In February 1991 he met actress Jennifer Mary Butala (Jenna Elfman) during an audition for a Sprite commercial. Four years later they were married on February 18, 1995. Bodhi is of Jewish descent, and Jenna was raised Catholic. When they met he was a practicing Scientologist. Jenna became a Scientologist after her husband introduced her to its teachings. As of 2018, both were active Scientologists.

In 2000, Bodhi and Jenna Elfman bought a 5,000-square-foot (460 m) 1920s home on gated two-acres in the Hollywood Hills from Madonna, for US$4 million, which they sold on in April 2004 for US$4.7 million to actress Katey Sagal, of Married… with Children fame.

Their first child, son Story Elias Elfman, was born on July 23, 2007. Their second son, Easton Quinn Monroe Elfman, was born on March 2, 2010.

In 2012, Elfman and his wife, Jenna, started their podcast, Kicking and Screaming by Jenna and Bodhi Elfman.