William Hooper was an Episcopalian.
He was identified as an Episcopalian by the North Carolina State Library. (Source: Ian Dorion, "Table of the Religious Affiliations of American Founders", 1997).
From: Robert G. Ferris (editor), Signers of the Declaration: Historic Places Commemorating the Signing of the Declaration of Independence, published by the United States Department of the Interior, National Park Service: Washington, D.C. (revised edition 1975), page 77:
Hooper was born in Boston, Mass., in 1742, the first child of William Hooper, a Scoth immigrant and Congregationalist clergyman who 5 years later was to transfer to the Anglican Church. Groomed for the ministry in his youth, Hooper undertook 7 years of preparatory education at Boston Latin School. This qualified him in 1757 to enter Harvard College in the sophomore class. He graduated 3 years later, but much to the chagrin of his father rejected the ministry as a profession. The next year, he further alienated his Loyalist father and isolated himself from his family by taking up the study of law under James Otis, a brilliant but radical lawyer.
Note that numerous sources and authoritative references have been consulted in order to ascertain the religious affiliation of the American Founding Fathers. Note that the excerpts and references mentioned on this page are not the only references used in order to identify this person's religious affiliation.