Stone graduated from Williams College in 1952. He received a master's degree from the Yale University School of Drama in 1955, at which time he joined a CBS training program. Before helping to create Sesame Street, he worked on the popular children's television show Captain Kangaroo for CBS. He also worked on several other Muppet projects before and during his time on Sesame Street, and was the author of several books including the popular "The Monster at the End of this Book". He was married for 9 years to actress Beverly Owen.
Stone was Sesame Street's principal director until 1996. Working with Jim Henson, he helped to create many of the Muppet characters, including Big Bird and Cookie Monster. He was also responsible for the show's format and setting. Stone contributed occasional announcer voices (such as the soap opera promo spoof "School in the Afternoon"), and served similar duty on two Muppet Meeting Films. In April 1990, Stone hosted and directed a television special titled Sing! Sesame Street Remembers Joe Raposo and His Music. The special was created as a tribute to Joe Raposo, who passed away from lymphoma in February 1989.
Jon Stone died of complications from Lou Gehrig's disease on March 30th, 1997. In his New York Times obituary, Joan Ganz Cooney describes Stone as "probably the most brilliant writer of children's television material in America."