Pepper remained active in national church affairs, including several times as General Convention delegate. He served on the Board of Missions (where he worked with J. Pierpont Morgan and learned to admire Bishop Charles Henry Brent. He also served on the General Board of Religious Education (GBRE) with bishops Ethelbert Talbot, Chauncey Brewster, David H. Greer, Thomas F. Gailor and Edward L. Parsons, as well as distinguished laymen Nicholas Murray Butler (president of Columbia University) and Robert Hallowell Gardiner III. Pepper became the Episcopal delegate to the World Conference of Faith and Order. He also helped finance and organize the building of the Washington National Cathedral.