Henry Clay Folger, Jr. was born in New York City to Henry Clay Folger, Sr. of Nantucket, MA and Eliza Jane (Clark) Folger of New York, the oldest of their eight children.
He prepared at Adelphi Academy, Brooklyn, New York, where he was acquainted with Charles Pratt, the businessman and president of the Adelphi board of trustees who became a mentor to Folger.