John Leddy Phelan was born in Fall River, Massachusetts to an Irish American family.
Phelan graduated from Harvard College cum laude in History in 1947; he earned his doctorate at University of California, Berkeley in 1951.
His dissertation on the Franciscan Order in early colonial Mexico became the basis for his first book, The Millennial Kingdom of the Franciscans in the New World: A Study of the Writings of Gerónimo de Mendieta (1525-1604) (1956, 2nd edition 1970), which remains an important work in the field of early Latin America.
His third monograph, The Kingdom of Quito in the Seventeenth Century: Bureaucratic Politics in the Spanish Empire (1967)[2] is a mixture of political and social history, along with an important chapter on cultural history focusing on Mariana de Jesús de Paredes, known as the "Lily of Quito."
In 1968 the book was accorded honorable mention for the Bolton Prize of the Conference on Latin American History.