Wentz was born Peter Lewis Kingston Wentz III, in Wilmette, Illinois, an affluent suburb of Chicago. He is the son of Dale (nee Lewis), a high school admissions counselor, and Pete Wentz II, an attorney. He is of English and German descent on his father's side and Afro-Jamaican on his mother's side. He has a younger sister, Hillary, and a younger brother, Andrew.

Wentz has bipolar disorder, and has taken medication for it since he was eighteen. In February 2005, Wentz attempted suicide by taking an overdose of the anxiety medication Ativan, and as a result, spent a week in the hospital. Commenting on the event to a magazine, he said:  The suicide attempt was put into song form, "7 Minutes in Heaven (Atavan Halen)" and released on their album, From Under The Cork Tree. After this event, Wentz moved back in with his parents. Wentz later spoke of his suicide attempt to the support site Halfofus.com and cites Jeff Buckley's version of the Leonard Cohen classic "Hallelujah" as a song that saved his life.  In 2006, Wentz started dating singer Ashlee Simpson. In April 2008, Simpson and Wentz confirmed their engagement, and were married on May 17, 2008, at Simpson's parents' residence in Encino, California, with her father officiating the ceremony. Two weeks later, she confirmed her pregnancy. Her surname changed from Simpson to Wentz and she was briefly known professionally as Ashlee Simpson-Wentz. Simpson gave birth to their son on November 20, 2008.  On February 8, 2011, Simpson filed for divorce, citing "irreconcilable differences". She asked for joint custody and primary physical custody of their son with visitation for Wentz, along with spousal support. However, a later report said that Simpson believed the couple simply "married too young", with the source stating that, "It was honestly a classic case of marrying young, having a kid young and growing apart over the years". Wentz reportedly did not want the divorce. Their divorce was finalized on November 22, 2011.  On February 17, 2014, Wentz and his current girlfriend Meagan Camper announced that the couple were expecting their first child together and Wentz's second. Their son was born on August 21, 2014. On January 2, 2018 Wentz posted to his Instagram that he and Camper were expecting their second child together and Wentz's third, a girl.

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