Spacek was born on December 25, 1949, in Quitman, Texas, the daughter of Virginia Frances (née Spilman; December 18, 1917 – November 10, 1981) and Edwin Arnold Spacek Sr. (July 3, 1910 – January 7, 2001), a county agricultural agent. Spacek's father was of three quarters Czech (Moravian) and one quarter German ancestry; her paternal grandparents were Mary (Cervenka) and Arnold A. Spacek (who served as Mayor of Granger, Texas in Williamson County). Her mother, who was of English and Irish descent, was from the Rio Grande Valley of Texas. At age 6, she performed on stage for the first time, appearing in a local talent show. Although her birth name was Mary Elizabeth, she was always called Sissy by her brothers which led to her stage name. She attended Quitman High School and was named homecoming queen at her senior prom.
Spacek was greatly affected by the death of her close 18-year-old brother, Robbie, in 1967 from leukemia when she was 17, which she has called "the defining event of my whole life". Spacek said the personal tragedy made her fearless in her acting career: "I think it made me brave. Once you experience something like that, you've experienced the ultimate tragedy. And if you can continue, nothing else frightens you. That's what I meant about it being rocket fuel – I was fearless in a way. Maybe it gave more depth to my work because I had already experienced something profound and life-changing."