Kennedy died of whooping cough in 1909 at his home, 6 West 57 Street in New York. Honorary pallbearers at his funeral included, Stephen Baker, president of the Bank of Manhattan Company (son of Stephen Baker); Nicholas Murray Butler, president of Columbia University; Robert W. DeForest, president of the Charity Organization Society; Cleveland H. Dodge; Howard Elliot, president of the Northern Pacific Railway; Seth Low; J. Pierpont Morgan; George A. Morrison; former President of the St. Andrews Society; Henry L. Smith, John A. Stewart and Frederick Sturges, Vice President of the Presbyterian Hospital. Others present in the church for his funeral were Andrew Carnegie and his wife, Louise Whitfield Carnegie, Henry De Forest and Eugene Delano.