Fogerty was born in Berkeley, California, and grew up in El Cerrito, California, one of five sons born to Galen Robert and Edith Lucile Fogerty. His father was a native of South Dakota and worked as a Linotype operator for the Berkeley Gazette. Lucile Fogerty was from Great Falls, Montana. When John was two years old, his parents converted to Catholicism. He first attended a Catholic school in Berkeley named the School of the Madeleine. In his memoir, Fortunate Son, Fogerty was critical of the school, saying he was not permitted to go to the bathroom when he asked and frequently wet himself in the classroom and was forced to sit in his wet clothing.
After one year, he enrolled in nearby Harding Grammar School. In Fogerty's book, he stated that his parents were alcoholics and that they divorced when he was in the third or fourth grade. He later attended St. Mary's High School, then transferred to El Cerrito High School, where he met the other future members of CCR and took guitar lessons from Berkeley Folk Festival creator/producer Barry Olivier. Fogerty's older brother Tom was a guitarist and bandmate in the group that eventually became CCR. John Fogerty spent summer vacations at Putah Creek, near Winters, California, which became the subject of the CCR song "Green River".