Phillips was born in Texas City, Texas and raised in St. Louis, Missouri. His father, Victor, was a chemical engineer and his mother, Grace, was a teacher. Stone also has two siblings: a brother Vic, who is chairman of the college of Natural Resources at the University of Wisconsin Stevens-Point; and a sister Minta, a radiologist in Greensboro, NC and a graduate of Harvard Medical School. He attended Parkway West High School, where he won so many departmental awards (more than 10) that the school started limiting future students to winning only 2 awards. While attending college at Yale, he was a starting quarterback on the football team and graduated with a degree in philosophy. He was also a member of Yale's Scroll and Key society.
In 1986, Phillips landed his first major on-air role as a correspondent for 20/20. That year, he was also a substitute host on Good Morning America and a sports anchor on ABC’s World News Sunday. While at NBC News, Phillips also hosted Weekend Magazine with Stone Phillips. On October 17, 2005, Phillips was a guest on the premiere episode of The Colbert Report.