Gooding was born in The Bronx, New York, the son of Shirley, a singer with the Sweethearts, and Cuba Gooding, Sr., a lead vocalist of soul group The Main Ingredient. He has two brothers, Tommy Gooding (a musician) and fellow actor Omar Gooding. His family moved to Los Angeles after Gooding, Sr.'s music group had a hit single with "Everybody Plays the Fool" in 1972; the elder Gooding abandoned his family two years later. Cuba, Jr. became a born-again Christian at age 13. Gooding was raised by his mother and attended four different high schools (including North Hollywood High School, Tustin High School, Apple Valley High School, and John F. Kennedy High School in Granada Hills in Los Angeles). He served as class president in three of them. During his appearance on the The Howard Stern Show, Gooding, Jr. revealed that after his father had left, his family lived in hotels throughout Los Angeles.

Gooding has been married to Sara Kapfer since 1994; the two have known each other sin