Yankovic was born in Downey, California and raised in Lynwood, California. He is the only child of Mary Elizabeth (Vivalda) and Nick Yankovic. His father was born in Kansas City, Kansas, of Yugoslavian descent, and began living in California after serving during World War II; he believed "the key to success" was "doing for a living whatever makes you happy" and often reminded his son of this philosophy. Nick married Mary in 1949.

Yankovic changed his diet to become a vegan in 1992 after a former girlfriend gave him the book Diet for a New America and he felt "it made ... a very compelling argument for a strict vegetarian diet". When asked how he can "rationalize" performing at events such as the Great American Rib Cook-Off when he is a vegan, he replied, "The same way I can rationalize playing at a college even though I'm not a student anymore." In a 2011 interview with news website OnMilwaukee, Yankovic clarified his stance on his diet, saying, "I am still a vegetarian, and I try to be a vegan, but I occasionally cheat. If there's a cheese pizza on the band bus, I might sneak a piece."  Yankovic married Suzanne Krajewski in 2001 after being introduced by their mutual friend Bill Mumy. Their daughter, Nina, was born in 2003. Yankovic identifies as Christian and has stated that a couple from his church appeared on the cover of Poodle Hat. Yankovic's religious background is reflected in his abstinence from alcohol, tobacco, drugs, and profanity. He and his family currently live in Los Angeles in a house previously owned at separate times by Jack S. Margolis and Heavy D.  On April 9, 2004, Yankovic's parents were found dead in their Fallbrook, California home, the victims of accidental carbon monoxide poisoning from their fireplace. Several hours after his wife notified him of his parents' death, Yankovic went on with his concert in Appleton, Wisconsin, saying that "since my music had helped many of my fans through tough times, maybe it would work for me as well" and that it would "at least ... give me a break from sobbing all the time." Their deaths occurred following the release of Poodle Hat, which was Yankovic's lowest-selling album in 20 years, but he considered continuing the show and tour therapeutic, saying "if I didn't have anything to distract me, I probably would have spiraled into an even deeper depression. For a couple of hours each night, I could go onstage and put on a big fake smile and pretend like everything was just OK." In a 2014 interview, Yankovic called his parents' death "the worst thing that ever happened to me." He added, "I knew intellectually, that at some point, probably, I'd have to, you know, live through the death of my parents, but I never thought it would be at the same time, and so abruptly."

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