William Patrick Corgan Jr. was born at Columbus Hospital in the Lincoln Park neighborhood of Chicago on March 17, 1967, the oldest son of Martha Louise Maes Corgan Lutz and guitarist William Dale Corgan (1947–2021). He was raised Catholic. His parents had one more son, Ricky, before divorcing in 1970. His father was remarried to a flight attendant, and Corgan and his brother went to live with them in the Chicago suburb of Glendale Heights, Illinois. Corgan alleges that his stepmother was abusive to him, both physically and emotionally. He developed a protective bond with his younger paternal half-brother, Jesse, who had special needs as a child. When Corgan's father and stepmother separated, all three boys lived alone with their stepmother, and both of his birth parents lived separately within an hour's drive. Corgan described his father as a "drug dealing, gun-toting musician mad man". Although this had a huge negative impact on his childhood, in retrospect he respects his father as a great musician.

In 2005, Corgan took out a full-page ad in Chicago's two major newspapers (Chicago Tribune and The Chicago Sun-Times) revealing his desire to re-form the Smashing Pumpkins. Several days later, Jimmy Chamberlin accepted Corgan's offer for a reunion.

On April 20, 2006, the band's official website confirmed that the group was indeed reuniting. The re-formed Smashing Pumpkins went into studio for much of 2006 and early 2007, and performed its first show in seven years on May 22, 2007, with new members Ginger Pooley (bass) and Jeff Schroeder (guitar) replacing Wretzky and Iha. The new album, titled Zeitgeist, was released in the United States on July 10, 2007, and debuted at No. 2 on the Billboard charts. Corgan and the rest of the Pumpkins toured extensively throughout 2007 and 2008, also releasing the EP American Gothic and the singles "G.L.O.W." and "Superchrist". Chamberlin left the band in March 2009, and Corgan elected to continue under the name.

For much of his life, Corgan has struggled with anxiety, depression, panic attacks, self-harm, obsessive-compulsive disorder, and suicidal ideation. He attributes these problems to the abuse he endured as a child at the hands of his father and stepmother, as well as other personal issues. He has since become an advocate for abuse support networks.

Corgan is an avid supporter of the Chicago Cubs, and an occasional commentator on the team for WXRT DJ Lin Brehmer. He has appeared at many Cubs games, occasionally throwing the ceremonial first pitch or singing "Take Me Out to the Ballgame". He is also a fan of the Chicago Bulls, Chicago Blackhawks and Chicago Bears, and became personal friends with Dennis Rodman and Chris Chelios. He is an avid professional wrestling fan and appeared at an ECW event wielding an acoustic guitar as a weapon. In 2008, the Pumpkins song "Doomsday Clock" was used by ROH for promotional videos. On April 26, 2010, Corgan appeared on the SIRIUS Satellite Radio program Right After Wrestling with Arda Ocal to discuss his love for wrestling and the importance of unique theme songs for characters. On August 26, 2010, he took part in a storyline with AAA during a concert for MTV World Stage. As far as other entertainment, Corgan once commented that all he watches on TV are "sports and the Three Stooges". In March 2008, he was spotted in the crowd at the final day of the cricket test match between New Zealand and England.

Corgan accepts some elements of Catholicism, Buddhism, and Ken Wilber's spiritual ideas. In 2009, he launched Everything From Here to There, an interfaith website that is devoted to "Mind-Body-Soul" integration. He mentions praying each morning and night to be able to see through Jesus Christ's eyes and feel with his heart. An analysis of the symbolism of Corgan's lyrics considered the blend of beliefs he has cited in various interviews, which include ideas about religion, multiple dimensions, and psychic phenomena. In an interview on the Howard Stern Show, Corgan claimed to have once had an encounter with a person who had the ability to shapeshift.

Corgan's mother Martha died in December 1996. The song "For Martha", from Adore, was written in her memory. In the early 2000s Corgan named his label Martha's Music after her as well. A picture of Martha as a young girl sitting on a fake moon at Riverview Park is featured on the flipside of the Siamese Dream booklet.

In 1991, Corgan briefly dated musician and actress Courtney Love. In an interview on The Howard Stern Show, Corgan confessed that he arranged for Love's band to stay in his Chicago apartment in order to meet her, an encounter he had longed for after seeing her photograph on the back of Hole's new single. Their relationship ended on October 12, 1991, when Love found out that Corgan had another relationship.