Bening was born in Topeka, Kansas, the daughter of Shirley Katherine (née Ashley; b. 1929) and Arnett Grant Bening (b. 1926). Her mother was a church singer and soloist, and her father was a sales training consultant and insurance salesman. Her parents, natives of Iowa, were practicing Episcopalians and conservative Republicans. She is of mostly German and English descent.
The youngest of four children, she has an older sister Jane (b. 1953), two older brothers Bradley (b. 1955) and Byron (b. 1957). The family moved to Wichita, Kansas in 1959, where she spent her early childhood. In 1965, her father took a job with a company in San Diego, California, and they moved there.
She began acting in junior high school, playing the lead in The Sound of Music. She graduated in 1975 from Patrick Henry High School, where she studied drama. She then spent a year working as a cook on a charter boat taking fishing parties out on the Pacific Ocean, and scuba diving for recreation. Bening attended San Diego Mesa College, then completed an academic degree in theatre arts at San Francisco State University.