Sebastian was born in Greenwich Village in New York City. His father, also John Sebastian, was a noted classical harmonica player and his mother was a radio script writer. He grew up surrounded by music and musicians, including Burl Ives and Woody Guthrie and hearing such players as Leadbelly and Mississippi John Hurt in his own neighborhood.
He came up through the Even Dozen Jug Band and the Mugwumps, which split to form the Lovin' Spoonful and the Mamas and Papas. Sebastian was joined by Zal Yanovsky in the Spoonful, which was named after a Mississippi John Hurt song.
The band became part of the American response to the British Invasion and was noted for such folk-flavored hits as "Jug Band Music", "Do You Believe in Magic," "Summer In the City," "Daydream," "Nashville Cats," "Did You Ever have to Make Up Your Mind," "Six O?Clock" and "Younger Girl".
Sebastian later had a hit with the theme song to the Welcome Back, Kotter TV show and has recently played with John Sebastian and the J-Band, a jug band including Fritz Richmond from the Even Dozen Jug Band, Yank Rachell, an original jug-band leader, and Geoff Muldaur.