From 1898 to 1904 he was president of the American Federation of Zionists, and worked with both Stephen S. Wise and Jacob De Haas as organizational secretaries. Though he was ever desirous of returning to the quiet life of academia, Gottheil attended the second Zionist Congress in Basel establishing relationships with Theodor Herzl and Max Nordau. "Professor Gottheil shunned publicity; he did not mind the trickles of adulation accorded him as President; but his official duties irked him beyond endurance. He hated to preside at meetings. He was careless in procedural matters and embarrassed by ceremonies in which he had to take part. He was horrified by emotional debates. He felt that his status as a professor was being sullied by his being President of a propaganda organization. He ran away from official duties. He usually limited his official addresses at Zionist meetings to the necessary items, speaking briefly. He became more and more nerve-provoked by his status, especially as the practical affairs of the Zionist Federation made no visible progress. Gottheil virtually vanished from the Zionist movement for the rest of his life. He continued writing and supporting the Zionist effort but he never again undertook a leadership role.
After 1904 he was vice president of the American Jewish Historical Society. Professor Gottheil wrote many articles on Oriental and Jewish questions for newspapers and reviews. He edited the Columbia University Oriental Series, and the Semitic Study Series. After 1901 he was one of the editors of the Jewish Encyclœpedia. He wrote: