The Rev. Luis Leon of St. John's Church has been chosen for the honour. He replaces Atlanta megachurch pastor Louie Giglio, who withdrew from the ceremony last week after a sermon he gave years ago surfaced in which he condemned gay relationships.
A Presidential Inaugural Committee spokeswoman, Addie Whisenant, had said that the person chosen to give the prayer would reflect the administration's beliefs. The Episcopal Church blesses same-sex relationships and elects bishops who live openly with same-gender partners.
Every president since James Madison, including Obama, has attended a service at St. John's Church, which stands across from the White House on Lafayette Square. Leon is a native of Cuba who came to the United States at age 12. He delivered prayers at the 2005 inauguration of President George W. Bush.
The presidential inaugural will be held Monday.